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Package 525/671HostnameOS / ArchBUILDCHECKBUILD BIN
Rbowtie 1.0.2
Michael Stadler
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Rbowtie
Last Changed Rev: 75650 / Revision: 76155
Last Changed Date: 2013-04-15 05:37:40 -0700 (Mon, 15 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: Rbowtie
Version: 1.0.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rbowtie_1.0.2.tar.gz
StartedAt: 2013-05-01 09:57:41 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 09:59:08 -0700 (Wed, 01 May 2013)
EllapsedTime: 86.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Rbowtie.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Rbowtie.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Rbowtie/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rbowtie' version '1.0.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'Rbowtie' can be installed ... [46s/49s] WARNING
Found the following significant warnings:
  getSpliceMapUnmapped.cpp:188:15: warning: variable 'nbIn' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
See '/Users/biocbuild/bbs-2.12-bioc/meat/Rbowtie.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  7.2Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [13s/15s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
Rbowtie   7.561  0.664   8.561
SpliceMap 3.740  0.392   5.561
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/Rbowtie.Rcheck/00check.log'
for details.

Rbowtie.Rcheck/00install.out:

* installing *source* package 'Rbowtie' ...
** libs
** arch - 
clang++ -O3  -DCOMPILER_OPTIONS="\"-O3   -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion\""  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion  \
		-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
		-I SeqAn-1.1 \
		-o bowtie-build ebwt_build.cpp \
		ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
		-lpthread 
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:52:
SeqAn-1.1/seqan/basic/basic_profile.h:161:14: warning: implicit conversion changes signedness: '_proInt' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
        return (_proData<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:54:
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:70:22: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
        const int DEFAULT = ˜(˜0u >> 1); // initialize with the smallest int
                  ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:229:116: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
                finline static void run(unsigned char* ptr, unsigned char c) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
                                                                                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1131:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1140:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char)c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1149:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1167:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1178:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna5<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1187:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1196:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1205:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna5<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1226:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Iupac<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1235:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1244:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1251:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1258:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1269:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_AA<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1278:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1287:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:83:
SeqAn-1.1/seqan/index/shape_gapped.h:583:12: warning: implicit conversion changes signedness: 'unsigned int' to 'typename Value<String<int, Alloc<void> > >::Type' (aka 'int') [-Wsign-conversion]
                                *itS = diff;
                                     ˜ ^˜˜˜
In file included from ebwt_build.cpp:7:
In file included from SeqAn-1.1/seqan/file.h:46:
SeqAn-1.1/seqan/file/cstream.h:142:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return getc(source);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:170:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:181:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:193:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
SeqAn-1.1/seqan/file/cstream.h:205:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
In file included from ebwt_build.cpp:9:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from ebwt_build.cpp:10:
./endian_swap.h:23:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        tmp |= ((u << 24) & (0xff << 24));
                          ˜  ˜˜˜˜˜^˜˜˜˜
./endian_swap.h:32:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 56) & (0xffull <<  0));
                             ^
./endian_swap.h:33:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 40) & (0xffull <<  8));
                             ^
./endian_swap.h:34:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 24) & (0xffull << 16));
                             ^
./endian_swap.h:35:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >>  8) & (0xffull << 24));
                             ^
./endian_swap.h:36:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u <<  8) & (0xffull << 32));
                             ^
./endian_swap.h:37:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 24) & (0xffull << 40));
                             ^
./endian_swap.h:38:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 40) & (0xffull << 48));
                             ^
./endian_swap.h:39:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 56) & (0xffull << 56));
                             ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:26:
./bitpack.h:26:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        thirty2 |= (two << (off*2));
                ˜˜  ˜˜˜˜^˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
In file included from ./pat.h:17:
In file included from ./threading.h:5:
./tinythread.h:631:9: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
typedef long long __intmax_t;
        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
In file included from ./pat.h:18:
./filebuf.h:73:61: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(_lastn_cur < LASTN_BUF_SZ) _lastn_buf[_lastn_cur++] = c;
                                                                               ˜ ^
./filebuf.h:158:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _inf->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:161:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _ins->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:478:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = slen;
                                     ˜ ^˜˜˜
./filebuf.h:505:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = len;
                                     ˜ ^˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
In file included from ./pat.h:19:
./qual.h:93:40: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
                char cc = solexaToPhred((int)c - 64) + 33;
                     ˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./qual.h:147:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return (int)pQ;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜
./qual.h:161:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:165:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./qual.h:188:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:191:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
In file included from ./pat.h:20:
In file included from ./hit_set.h:16:
./edit.h:36:7: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                   ˜^˜
./edit.h:36:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                      ˜^˜
./edit.h:36:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                               ˜^˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
In file included from ./pat.h:20:
./hit_set.h:37:12: warning: implicit conversion changes signedness: 'const uint8_t' (aka 'const unsigned char') to 'char' [-Wsign-conversion]
                fb.write(fw);
                ˜˜       ^˜
./hit_set.h:44:17: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t sz = edits.size();
                         ˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:50:8: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                sz = cedits.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:63:8: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                fw = fb.get();
                   ˜ ^˜˜˜˜˜˜˜
./hit_set.h:65:13: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                stratum = fb.get();
                        ˜ ^˜˜˜˜˜˜˜
./hit_set.h:244:16: warning: implicit conversion loses integer precision: 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t i = seqan::length(name);
                         ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:248:7: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = seqan::length(seq);
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:256:7: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = ents.size();
                  ˜ ^˜˜˜˜˜˜˜˜˜˜
./hit_set.h:298:18: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                maxedStratum = fb.get();
                             ˜ ^˜˜˜˜˜˜˜
./hit_set.h:391:29: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                ents.erase(ents.begin() + i);
                           ˜˜˜˜           ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
./pat.h:53:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:61:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:70:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:167:10: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                return seqan::length(patFw);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:723:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t ret = 0llu;
                               ^
./pat.h:728:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                return make_pair(ret, 0llu);
                                      ^
./pat.h:875:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                ^
./pat.h:875:32: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                             ^
./pat.h:1087:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1105:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1126:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, length);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1128:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, length);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:1129:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                itoa10(patid, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜
./pat.h:1164:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1169:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1183:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                patid_ += numthreads_;
                       ˜˜ ^˜˜˜˜˜˜˜˜˜˜
./pat.h:1188:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1189:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1358:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        s.erase(0, mytrim5);
                                        ˜          ^˜˜˜˜˜˜
./pat.h:1362:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        s.erase(s.length()-trim3_);
                                                          ˜^˜˜˜˜˜
./pat.h:1374:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        vq.erase(0, mytrim5);
                                        ˜˜          ^˜˜˜˜˜˜
./pat.h:1378:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        vq.erase(vq.length()-trim3_);
                                                            ˜^˜˜˜˜˜
./pat.h:1425:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1467:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1824:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:1829:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1847:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:1848:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:1871:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1892:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1898:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1887:21: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                patid = readCnt_-1;
                                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:1895:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:1897:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:1902:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2031:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2081:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2124:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2161:44: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(r2 != NULL) (*r2).nameBuf[nameLen] = c;
                                                              ˜ ^
./pat.h:2162:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:2165:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2168:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength((*r2).name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2175:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2179:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength((*r2).name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2172:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2174:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2177:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, (*r2).nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2208:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2209:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2240:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2264:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2276:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                c2 = c;
                                   ˜ ^
./pat.h:2284:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2286:25: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                c = charToPhred33(c, solQuals_, phred64Quals_);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2288:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.qualBuf[off] = c;
                                                               ˜ ^
./pat.h:2300:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2303:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        c2 = c;
                           ˜ ^
./pat.h:2332:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                nameChars_(0), bufCur_(0), subReadCnt_(0llu)
                                                       ^
./pat.h:2361:32: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                nameBuf_[nameChars_++] = c;
                                                                       ˜ ^
./pat.h:2379:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        buf_[bufCur_++] = c;
                                                        ˜ ^
./pat.h:2408:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
                                        itoa10(readCnt_ - subReadCnt_, &r.nameBuf[nameChars_]);
                                        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2414:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        patid = readCnt_-1;
                                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2574:28: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                r.nameBuf[nameLen++] = c;
                                                     ˜ ^
./pat.h:2578:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _setLength(r.name, nameLen);
                                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2586:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2608:18: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.primer = c;
                                                         ˜ ^
./pat.h:2609:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.trimc = c2;
                                                        ˜ ^˜
./pat.h:2664:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.patFw, dstLen);
                        ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:2683:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = qualsRead - mytrim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2702:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2731:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = (*qualsReadCur) - trim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2733:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        c = charToPhred33(c, solQuals_, phred64Quals_);
                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2735:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        qbuf[off] = c;
                                                                  ˜ ^
./pat.h:2755:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2792:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altPatFw[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜
./pat.h:2794:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altQual[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜
./pat.h:2816:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2813:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, r.nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2815:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                nameLen = strlen(r.nameBuf);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2822:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2929:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2930:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2944:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                size_t len = dstLen - mytrim5;
                                       ˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2959:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2961:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2973:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2970:10: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                itoa10(readCnt_, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2972:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                nameLen = strlen(r.nameBuf);
                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2976:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:3062:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
./sequence_io.h:115:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        int64_t i = 0xffffffffll;
                    ^
./sequence_io.h:138:26: warning: implicit conversion changes signedness: 'int64_t' (aka 'long long') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        stmp = stmp.substr(0, baseCutoff);
                               ˜˜˜˜           ^˜˜˜˜˜˜˜˜˜
./sequence_io.h:170:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        int64_t i = 0xffffffffll;
                    ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:651:14: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        size_t a = (rand() % n) + begin; // choose pivot between begin and end
                    ^˜˜˜˜˜ ˜
./multikey_qsort.h:748:14: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        size_t a = (rand() % n) + begin; // choose pivot between begin and end
                    ^˜˜˜˜˜ ˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:9:
./timer.h:34:40: warning: implicit conversion loses integer precision: 'long' to 'unsigned int' [-Wshorten-64-to-32]
                unsigned int hours   = (passed / 60) / 60;
                             ˜˜˜˜˜     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:16:21: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define VMSG_NL(args...) \
                    ^
./diff_sample.h:25:18: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define VMSG(args...) \
                 ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:17:
./zbox.h:48:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                z[k] = betaLen + q;
                                               ˜ ^
./zbox.h:50:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                rCur = rCur + q;
                                            ˜ ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:29:
./word_io.h:119:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return endianSwapI32(x);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./word_io.h:121:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return x;
                ˜˜˜˜˜˜ ^
./word_io.h:135:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return endianSwapI32(x);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./word_io.h:137:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return x;
                ˜˜˜˜˜˜ ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:31:
In file included from ./hit.h:15:
./bitset.h:23:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                sz &= ˜31;            // Make sure it's 32-aligned
                   ˜˜ ^˜˜
./bitset.h:511:17: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        oss << (test(i)? "1" : "0");
                                ˜˜˜˜ ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:31:
./hit.h:181:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                memset(ents_, 0, len_ << 2);
                                ˜˜˜˜˜˜           ˜˜˜˜˜^˜˜˜
./hit.h:204:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                ii = h.length() - ii - 1;
                                                ˜ ^˜
./hit.h:208:18: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        if(h.mms.test(i)) {
                           ˜          ^
./hit.h:209:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                rc = charToDna5[(int)h.refcs[i]];
                                                     ˜       ^
./hit.h:204:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                                ii = h.length() - ii - 1;
                                   ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./hit.h:316:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numAligned_(0llu),
                            ^
./hit.h:317:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numUnaligned_(0llu),
                              ^
./hit.h:318:13: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numMaxed_(0llu),
                          ^
./hit.h:319:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numReported_(0llu),
                             ^
./hit.h:320:22: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numReportedPaired_(0llu),
                                   ^
./hit.h:421:22: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                        sort(hs.begin() + start, hs.begin() + end);
                             ˜˜           ^˜˜˜˜
./hit.h:421:42: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                        sort(hs.begin() + start, hs.begin() + end);
                                                 ˜˜           ^˜˜
./hit.h:438:35: warning: implicit conversion changes signedness: 'streamoff' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        out(h.h.first).writeChars(buf, ss.tellp());
                        ˜˜˜                            ^˜˜˜˜˜˜˜˜˜
./hit.h:623:51: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:625:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:647:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:648:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:650:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:651:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:677:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:679:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:699:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:700:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:702:58: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:703:58: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:730:52: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:732:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:752:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:753:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:755:57: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:756:57: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:971:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                _numValidHits(0llu),
                              ^
./hit.h:1021:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        ret = _bufferedHits.size();
                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:1336:40: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        _bufferedHits[i].oms = (sz / mult_) - 1;
                                             ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./hit.h:1519:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                ss << "<" << h.h.first << "," << (h.h.second + offBase) << "," << h.mms.count();
                                                             ˜ ^˜˜˜˜˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:32:
./ref_read.h:173:31: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                if (name) name->push_back(c);
                                          ˜˜˜˜            ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:40:
./reference.h:84:41: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        mmFile = (char*)mmap((void *)0, sbuf.st_size,
                                        ˜˜˜˜            ˜˜˜˜˜^˜˜˜˜˜˜
./reference.h:313:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 0) & 3) << 24;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./reference.h:314:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 2) & 3) << 16;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./reference.h:315:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 4) & 3) << 8;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./reference.h:316:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 6) & 3) << 0;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./reference.h:318:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 0) & 3) << 0;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./reference.h:319:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 2) & 3) << 8;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./reference.h:320:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 4) & 3) << 16;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./reference.h:321:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 6) & 3) << 24;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./reference.h:225:25: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const value_type' (aka 'const unsigned int') [-Wshorten-64-to-32]
                refRecOffs_.push_back(recs_.size());
                ˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜˜
./reference.h:579:17: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
                                                        count -= chars;
                                                              ˜˜ ^˜˜˜˜
./reference.h:580:18: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
                                                        bufOff += chars;
                                                               ˜˜ ^˜˜˜˜
./reference.h:581:16: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
                                                        toff += chars;
                                                             ˜˜ ^˜˜˜˜
In file included from ebwt_build.cpp:11:
./ebwt.h:126:25: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                _eftabLen = _ftabChars*2;
                          ˜ ˜˜˜˜˜˜˜˜˜˜^˜
./ebwt.h:135:23: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
                _sideSz = _lineSz * _linesPerSide;
                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:140:27: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
                _numLines = _numSides * _linesPerSide;
                                      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1285:17: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                hit.stratum = stratum;
                            ˜ ^˜˜˜˜˜˜
./ebwt.h:1307:24: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.crefcs[off] = refcs[i];
                                                        ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1310:22: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.crefcs[i] = refcs[i];
                                                      ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1331:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        read[i] = (int)hit.patSeq[i];
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1332:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                        qual[i] = mmPenalty(maqRound, phredCharToPhredQual(hit.quals[i]));
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1340:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                rf[i] = (1 << rf[i]);
                                      ˜  ˜˜^˜˜˜˜˜˜˜
./ebwt.h:1356:39: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        size_t nqlen = qlen + (colExEnds ? -1 : 1);
                                            ˜              ^˜
./ebwt.h:1427:23: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.refcs[off] = refcs[i];
                                                       ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1430:29: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.refcs[mmui32[i]] = refcs[i];
                                                             ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1538:34: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        lbot._charOff = ltop._charOff + spread;
                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./ebwt.h:1544:50: warning: implicit conversion loses integer precision: 'unsigned int' to 'int16_t' (aka 'short') [-Wconversion]
                        if(!lbot._fw) lbot._by = sideBwtSz - lbot._by - 1;
                                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:1544:46: warning: implicit conversion changes signedness: 'int16_t' (aka 'short') to 'unsigned int' [-Wsign-conversion]
                        if(!lbot._fw) lbot._by = sideBwtSz - lbot._by - 1;
                                                           ˜ ˜˜˜˜˜^˜˜
./ebwt.h:1576:30: warning: implicit conversion loses integer precision: 'unsigned int' to 'int16_t' (aka 'short') [-Wconversion]
                        _by = ep._sideBwtSz - _by - 1;
                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:1576:26: warning: implicit conversion changes signedness: 'int16_t' (aka 'short') to 'unsigned int' [-Wsign-conversion]
                        _by = ep._sideBwtSz - _by - 1;
                                            ˜ ^˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:1607:
In file included from ./ebwt_search_backtrack.h:8:
./ebwt_search_util.h:202:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        al.u64.u64 = 0xffffffffffffffffllu;
                                     ^
./ebwt_search_util.h:266:26: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        uint32_t off = al.off.off;
                                 ˜˜˜   ˜˜˜˜˜˜˜^˜˜
./ebwt_search_util.h:324:26: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                uint16_t tpos0 = plen-1-pos0;
                         ˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜
./ebwt_search_util.h:330:51: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                appendValue(muts, QueryMutation(tpos0, oldChar, chr0)); // apply mutation
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜
./ebwt_search_util.h:335:27: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        uint16_t tpos1 = plen-1-pos1;
                                 ˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜
./ebwt_search_util.h:342:52: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                        appendValue(muts, QueryMutation(tpos1, oldChar, chr1)); // apply mutation
                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜
./ebwt_search_util.h:347:28: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                uint16_t tpos2 = plen-1-pos2;
                                         ˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜
./ebwt_search_util.h:355:48: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                                append(muts, QueryMutation(tpos2, oldChar, chr2)); // apply mutation
                                             ˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜
./ebwt_search_util.h:317:19: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t plen = length(seq);
                         ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:1607:
In file included from ./ebwt_search_backtrack.h:10:
./range_source.h:56:56: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        yetMoreEdits_ = pool.alloc(qlen + 10 - numMoreEdits - numEdits);
                                        ˜˜˜˜       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
./range_source.h:138:55: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        epool.free(yetMoreEdits_, qlen + 10 - numMoreEdits - numEdits);
                        ˜˜˜˜˜                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
./range_source.h:326:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                ret.pos = pos;
                        ˜ ^˜˜
./range_source.h:496:23: warning: operand of ? changes signedness: 'const char' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                ret.chr = color ? "0123"[chr] : "ACGT"[chr];
                                        ˜         ^˜˜˜˜˜˜˜˜˜˜
./range_source.h:496:37: warning: operand of ? changes signedness: 'const char' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                ret.chr = color ? "0123"[chr] : "ACGT"[chr];
                                        ˜                       ^˜˜˜˜˜˜˜˜˜˜
./range_source.h:515:22: warning: operand of ? changes signedness: 'const char' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        ret.chr = color ? "0123"[chr] : "ACGT"[chr];
                                ˜         ^˜˜˜˜˜˜˜˜˜˜
./range_source.h:515:36: warning: operand of ? changes signedness: 'const char' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        ret.chr = color ? "0123"[chr] : "ACGT"[chr];
                                ˜                       ^˜˜˜˜˜˜˜˜˜˜
./range_source.h:611:21: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        rangesSz_ = qlen - rdepth_;
                                  ˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜
./range_source.h:766:23: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        r = rand.nextU32() % numTiedPositions;
                          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./range_source.h:766:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        r = rand.nextU32() % numTiedPositions;
                                           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./range_source.h:779:38: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                uint16_t newRdepth = rdepth_ + pos + 1;
                         ˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./range_source.h:782:24: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                uint16_t depth = pos + rdepth_;
                         ˜˜˜˜˜   ˜˜˜˜^˜˜˜˜˜˜˜˜
./range_source.h:795:31: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                newRdepth, 0, cost_, ham_ + hamadd,
                                                     ˜˜˜˜˜^˜˜˜˜˜˜˜
./range_source.h:1636:43: warning: extra ';' inside a class [-Wextra-semi]
        ASSERT_ONLY(std::set<Branch*> branchSet_);
                                                 ^
./range_source.h:1699:54: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                foundRange(false), done(_done), minCostAdjustment_(minCostAdjustment)
                                                                  ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./range_source.h:1968:41: warning: extra ';' inside a class [-Wextra-semi]
        ASSERT_ONLY(std::set<int64_t> allTops_);
                                               ^
./range_source.h:2552:43: warning: extra ';' inside a class [-Wextra-semi]
        ASSERT_ONLY(std::set<int64_t> allTopsRc_);
                                                 ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:1607:
./ebwt_search_backtrack.h:1208:37: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        uint64_t prehits = 0xffffffffffffffffllu)
                                           ^
./ebwt_search_backtrack.h:74:11: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                _maxBts(maxBts),
                       ˜^˜˜˜˜˜
./ebwt_search_backtrack.h:79:10: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                _ihits(0llu)
                       ^
./ebwt_search_backtrack.h:223:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const unsigned int' [-Wshorten-64-to-32]
                _qlen = min<uint32_t>(length(*_qry), qlen);
                        ˜˜˜           ^˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:274:41: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        ret = reportAlignment(0, top, bot, ham);
                                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜              ^˜˜
./ebwt_search_backtrack.h:278:21: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                ret = backtrack(ftabChars, // depth
                                      ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:257:41: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const unsigned int' [-Wshorten-64-to-32]
                uint32_t m = min<uint32_t>(_unrevOff, _qlen);
                             ˜˜˜                      ^˜˜˜˜
./ebwt_search_backtrack.h:545:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        top = pairTop(pairs, d, c); bot = pairBot(pairs, d, c);
                                              ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:545:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        top = pairTop(pairs, d, c); bot = pairBot(pairs, d, c);
                                                                          ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:555:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        top = pairTop(pairs, d, c); bot = pairBot(pairs, d, c);
                                              ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:555:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        top = pairTop(pairs, d, c); bot = pairBot(pairs, d, c);
                                                                          ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:588:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        uint32_t spread = pairSpread(pairs, d, i);
                                                          ˜˜˜˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:612:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                eltop = pairTop(pairs, d, i);
                                                                        ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:613:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                elbot = pairBot(pairs, d, i);
                                                                        ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:734:54: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                bool ret = reportAlignment(stackDepth, top, bot, ham);
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                       ^˜˜
./ebwt_search_backtrack.h:833:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        j = btcint = elcint;
                                          ˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:898:23: warning: implicit conversion changes signedness: 'char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                        _refcs.push_back(btchar);
                                        ˜˜˜˜˜˜           ^˜˜˜˜˜
./ebwt_search_backtrack.h:900:27: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
                                        _refcs[stackDepth] = btchar;
                                                           ˜ ^˜˜˜˜˜
./ebwt_search_backtrack.h:911:56: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        ret = reportAlignment(stackDepth+1, bttop, btbot, btham);
                                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                             ^˜˜˜˜
./ebwt_search_backtrack.h:922:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        uint32_t ftabOff = (*_qry)[_qlen - ftabChars];
                                                                         ˜ ^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:927:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                                if(_qlen-j == icur) {
                                                        ˜^
./ebwt_search_backtrack.h:928:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                        ftabOff |= btcint;
                                                                ˜˜ ^˜˜˜˜˜
./ebwt_search_backtrack.h:931:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                                        ftabOff |= (uint32_t)(*_qry)[_qlen-j];
                                                                                          ˜^
./ebwt_search_backtrack.h:945:32: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                                ebwt._eh._ftabChars,
                                                                ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1031:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                                uint32_t spread = pairSpread(pairs, k, l);
                                                                                                  ˜˜˜˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:1046:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                                        eltop = pairTop(pairs, k, l);
                                                                                                ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:1047:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                                        elbot = pairBot(pairs, k, l);
                                                                                                ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:1092:48: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        ret = reportAlignment(stackDepth, top, bot, ham);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                       ^˜˜
./ebwt_search_backtrack.h:459:28: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t cur = _qlen - d - 1; // current offset into _qry
                         ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:699:36: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                uint32_t d = _qlen - _mms[i] - 1;
                                                         ˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:776:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                icur = _qlen - i - 1; // current offset into _qry
                                                     ˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:805:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                                                btcint = j;
                                                                                       ˜ ^
./ebwt_search_backtrack.h:844:22: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                icur = _qlen - i - 1; // current offset into _qry
                                     ˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:964:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                        i+1,         // start from next position after
                                                        ˜^˜
./ebwt_search_backtrack.h:1014:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                uint32_t kcur = _qlen - k - 1; // current offset into _qry
                                                         ˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1045:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                                                        eli = k;
                                                                                            ˜ ^
./ebwt_search_backtrack.h:1144:37: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                uint32_t depth = _qlen - mms[i] - 1;
                                         ˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1189:18: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                        elims[d] = (1 << c);
                                 ˜  ˜˜^˜˜˜
./ebwt_search_backtrack.h:1252:34: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        uint32_t d = _qlen - mms[i] - 1;
                                                 ˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1355:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                uint32_t ftabOff = (*_qry)[_qlen - ftabChars];
                                                 ˜ ^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1361:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        ftabOff |= (uint32_t)(*_qry)[_qlen-i];
                                                          ˜^
./ebwt_search_backtrack.h:1417:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        if(_mms.size() <= stackDepth + i) {
                                          ^˜˜˜˜˜˜˜˜˜ ˜
./ebwt_search_backtrack.h:1421:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                _mms[stackDepth + i] = (*_muts)[i].pos;
                                     ^˜˜˜˜˜˜˜˜˜ ˜
./ebwt_search_backtrack.h:1423:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        if(_refcs.size() <= stackDepth + i) {
                                            ^˜˜˜˜˜˜˜˜˜ ˜
./ebwt_search_backtrack.h:1425:22: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                _refcs.push_back("ACGT"[(*_muts)[i].newBase]);
                                ˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1427:12: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                _refcs[stackDepth + i] = "ACGT"[(*_muts)[i].newBase];
                                       ^˜˜˜˜˜˜˜˜˜ ˜
./ebwt_search_backtrack.h:1427:30: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
                                _refcs[stackDepth + i] = "ACGT"[(*_muts)[i].newBase];
                                                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1499:28: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        promotePartialMutations(stackDepth);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1506:41: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        hit = reportFullAlignment(stackDepth + numMuts, top, bot, stratum, cost);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1554:29: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                 _qlen, stratum, cost, _patid, _seed,
                                                 ^˜˜˜˜
./ebwt_search_backtrack.h:1591:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                al.u64.u64 = 0xffffffffffffffffllu;
                             ^
./ebwt_search_backtrack.h:1608:20: warning: implicit conversion changes signedness: 'int' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
                al.entry.char0 = c;
                               ˜ ^
./ebwt_search_backtrack.h:1624:21: warning: implicit conversion changes signedness: 'int' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
                        al.entry.char1 = c;
                                       ˜ ^
./ebwt_search_backtrack.h:1639:22: warning: implicit conversion changes signedness: 'int' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
                                al.entry.char2 = c;
                                               ˜ ^
./ebwt_search_backtrack.h:1602:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t ci = _qlen - _mms[0] - 1;
                         ˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1618:25: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        ci = _qlen - _mms[1] - 1;
                           ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1633:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                ci = _qlen - _mms[2] - 1;
                                   ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1682:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        uint32_t icur = _qlen - i - 1; // current offset into _qry
                                 ˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:2475:37: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        uint64_t prehits = 0xffffffffffffffffllu)
                                           ^
./ebwt_search_backtrack.h:1934:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const unsigned int' [-Wshorten-64-to-32]
                qlen_ = min<uint32_t>(length(*qry_), qlen);
                        ˜˜˜           ^˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2033:13: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        offRev0_, offRev1_, offRev2_, offRev3_,
                                        ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2033:23: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        offRev0_, offRev1_, offRev2_, offRev3_,
                                                  ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2033:33: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        offRev0_, offRev1_, offRev2_, offRev3_,
                                                            ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2033:43: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        offRev0_, offRev1_, offRev2_, offRev3_,
                                                                      ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2034:16: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        0, ftabChars, icost, iham, top, bot,
                                           ^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2060:12: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                offRev0_, offRev1_, offRev2_, offRev3_,
                                ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2060:22: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                offRev0_, offRev1_, offRev2_, offRev3_,
                                          ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2060:32: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                offRev0_, offRev1_, offRev2_, offRev3_,
                                                    ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2060:42: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                offRev0_, offRev1_, offRev2_, offRev3_,
                                                              ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1988:40: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const unsigned int' [-Wshorten-64-to-32]
                uint32_t m = min<uint32_t>(offRev0_, qlen_);
                             ˜˜˜                     ^˜˜˜˜
./ebwt_search_backtrack.h:2032:52: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        pm.rpool, pm.epool, pm.bpool.lastId(), qlen_,
                                                                               ^˜˜˜˜
./ebwt_search_backtrack.h:2059:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!b->init(pm.rpool, pm.epool, pm.bpool.lastId(), qlen_,
                            ˜                                              ^˜˜˜˜
./ebwt_search_backtrack.h:2144:27: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜                    ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2304:27: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜                    ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2337:32: warning: implicit conversion changes signedness: 'char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                        curRange_.refcs.push_back((char)br->edits_.get(i).chr);
                                        ˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2352:27: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜                    ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2356:27: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜                    ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2367:48: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        if(!pm.splitAndPrep(rand_, qlen_, qualLim_, depth3_,
                            ˜˜                                      ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2144:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜             ^˜˜˜˜
./ebwt_search_backtrack.h:2148:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        cur = qlen_ - depth - 1; // current offset into qry_
                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:2294:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        nedits = br->edits_.size();
                               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2304:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜             ^˜˜˜˜
./ebwt_search_backtrack.h:2336:60: warning: implicit conversion loses integer precision: 'unsigned long' to 'const value_type' (aka 'const unsigned int') [-Wshorten-64-to-32]
                                        curRange_.mms.push_back(qlen_ - br->edits_.get(i).pos - 1);
                                        ˜˜˜˜˜˜˜˜˜               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:2352:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜             ^˜˜˜˜
./ebwt_search_backtrack.h:2356:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜             ^˜˜˜˜
./ebwt_search_backtrack.h:2367:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!pm.splitAndPrep(rand_, qlen_, qualLim_, depth3_,
                            ˜˜                     ^˜˜˜˜
./ebwt_search_backtrack.h:2410:55: warning: implicit conversion loses integer precision: 'unsigned long' to 'const value_type' (aka 'const unsigned int') [-Wshorten-64-to-32]
                                curRange_.mms.push_back(qlen_ - seedRange_.mms[i] - 1);
                                ˜˜˜˜˜˜˜˜˜               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:2426:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t nedits = b->edits_.size();
                               ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2480:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t nedits = b->edits_.size();
                               ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2561:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                uint32_t ftabOff = (*qry_)[qlen_ - ftabChars];
                                                 ˜ ^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2567:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        ftabOff |= (uint32_t)(*qry_)[qlen_-i];
                                                          ˜^
./ebwt_search_backtrack.h:2795:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                lowAtPos = qual[qlen - d - 1];
                                                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2803:61: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                        minCost += mmPenalty(maqPenalty_, phredCharToPhredQual(lowQual));
                                                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2810:30: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        minCost = (seed_ ? 3 : 2) << 14;
                                ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./ebwt_search_backtrack.h:2819:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                lowAtPos = qual[qlen - d - 1];
                                                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2827:61: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                        minCost += mmPenalty(maqPenalty_, phredCharToPhredQual(lowQual1));
                                                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2836:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                lowAtPos = qual[qlen - d - 1];
                                                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2854:61: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                        minCost += mmPenalty(maqPenalty_, phredCharToPhredQual(lowQual2_1));
                                                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2856:62: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                minCost += mmPenalty(maqPenalty_, phredCharToPhredQual(lowQual2_2));
                                                                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2771:19: warning: implicit conversion loses integer precision: 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t qlen = seqan::length(qual);
                         ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:11:
./ebwt.h:1675:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        while(cur < (upToSide * eh._sideSz)) {
                     ^˜˜˜˜˜˜˜ ˜
./ebwt.h:1737:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memset(seen, 0, 4 * seenLen);
        ˜˜˜˜˜˜          ˜˜^˜˜˜˜˜˜˜˜
./ebwt.h:1868:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
   x = x - ((x >> 1) & 0x5555555555555555llu);
                       ^
./ebwt.h:1869:13: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
   x = (x & 0x3333333333333333llu) + ((x >> 2) & 0x3333333333333333llu);
            ^
./ebwt.h:1869:50: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
   x = (x & 0x3333333333333333llu) + ((x >> 2) & 0x3333333333333333llu);
                                                 ^
./ebwt.h:1870:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
   x = (x + (x >> 4)) & 0x0F0F0F0F0F0F0F0Fllu;
                        ^
./ebwt.h:1883:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        uint64_t dwA  = dw &  0xAAAAAAAAAAAAAAAAllu;
                              ^
./ebwt.h:1884:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        uint64_t dwNA = dw & ˜0xAAAAAAAAAAAAAAAAllu;
                              ^
./ebwt.h:1902:8: warning: implicit conversion changes signedness: 'int' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
        tmp = pop64(tmp); // Gets 7.62% in profile
            ˜ ^˜˜˜˜˜˜˜˜˜
./ebwt.h:1918:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        uint64_t dwA  = dw &  0xAAAAAAAAAAAAAAAAllu;
                              ^
./ebwt.h:1919:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        uint64_t dwNA = dw & ˜0xAAAAAAAAAAAAAAAAllu;
                              ^
./ebwt.h:1920:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        arrs[0] += (32 - pop64((dwA >> 1) | dwNA));
                ˜˜  ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1921:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        arrs[1] += pop64(˜(dwA >> 1) & dwNA);
                ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1922:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        arrs[2] += pop64((dwA >> 1) & ˜dwNA);
                ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1923:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        arrs[3] += pop64((dwA >> 1) & dwNA);
                ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1945:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                cCnt += countInU64(c, *(uint64_t*)&side[i]);
                     ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3588:18: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        uint32_t nPat = readI32(in, switchEndian); // nPat
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:4193:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        int sideCur = eh._sideBwtSz - 1;
            ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:4354:28: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        sideCur = eh._sideBwtSz - 1;
                                ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:4437:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        eftabLen = eh._ftabChars*2;
                 ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
ebwt_build.cpp:222:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                bmax = parseNumber<uint32_t>(1, "--bmax arg must be at least 1");
                                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ebwt_build.cpp:227:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                bmaxMultSqrt = parseNumber<uint32_t>(1, "--bmaxmultsqrt arg must be at least 1");
                                             ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ebwt_build.cpp:232:16: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                bmaxDivN = parseNumber<uint32_t>(1, "--bmaxdivn arg must be at least 1");
                                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ebwt_build.cpp:508:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                 << ", " << sizeof(long) << ", " << sizeof(long long)
                                                                           ^
ebwt_build.cpp:579:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                srand(seed);
                ˜˜˜˜˜ ^˜˜˜
ebwt_build.cpp:599:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        srand(seed);
                        ˜˜˜˜˜ ^˜˜˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:77:16: note: in instantiation of function template specialization 'seqan::length<char, seqan::Alloc<void> >' requested here
        size_t plen = length(path);
                      ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./alphabet.h:144:19: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >' requested here
        size_t readLen = seqan::length(read);
                         ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<char>' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<char>' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<char>' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<char>' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<char, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<char, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<char, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:278:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<char, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(name, sz);
                ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<seqan::SimpleType<unsigned char, seqan::_Dna5>, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:283:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(seq, sz);
                ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:90:
SeqAn-1.1/seqan/basic/basic_iterator_adapt_std.h:307:67: warning: implicit conversion changes signedness: 'unsigned long' to 'const difference_type' (aka 'const long') [-Wsign-conversion]
        return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) + right);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:764:76: note: in instantiation of function template specialization 'seqan::operator+<const std::basic_string<char>, unsigned long>' requested here
                        arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
                                                                                                ^
SeqAn-1.1/seqan/sequence/string_base.h:812:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, const std::basic_string<char> >' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:737:2: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char>, seqan::TagGenerous_>' requested here
        assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:70:3: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char> >' requested here
                assign(*this, source);
                ^
./pat.h:1391:17: note: in instantiation of function template specialization 'seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >::String<std::basic_string<char> >' requested here
                        v_.push_back(s);
                                     ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:323:17: warning: implicit conversion loses integer precision: 'const unsigned int' to 'unsigned char' [-Wconversion]
        target.value = source;
                     ˜ ^˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:82:3: note: in instantiation of function template specialization 'seqan::assign<unsigned char, seqan::_Dna, unsigned int>' requested here
                assign(*this, other);
                ^
SeqAn-1.1/seqan/sequence/string_packed.h:958:9: note: in instantiation of function template specialization 'seqan::SimpleType<unsigned char, seqan::_Dna>::SimpleType<unsigned int>' requested here
        return (value(hostIterator(me)) >> _bitpos(me)) & _PackedConsts<TContainer>::VALUE_MASK;
               ^
SeqAn-1.1/seqan/basic/basic_proxy.h:242:9: note: in instantiation of function template specialization 'seqan::getValue<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void> >' requested here
        return getValue(iter(me));
               ^
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:345:17: note: in instantiation of function template specialization 'seqan::getValue<seqan::IteratorProxy<seqan::Iter<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Packed<seqan::Alloc<void> > > > >' requested here
        target.value = getValue(source);
                       ^
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:82:3: note: in instantiation of function template specialization 'seqan::assign<unsigned char, seqan::_Dna, seqan::IteratorProxy<seqan::Iter<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Packed<seqan::Alloc<void> > > > >' requested here
                assign(*this, other);
                ^
./multikey_qsort.h:793:18: note: in instantiation of function template specialization 'seqan::SimpleType<unsigned char, seqan::_Dna>::SimpleType<seqan::Proxy<seqan::IteratorProxy<seqan::Iter<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Packed<seqan::Alloc<void> > > > > >' requested here
        return (uint8_t)(Dna)t[off];
                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./blockwise_sa.h:353:28: note: in instantiation of function template specialization 'seqan::length<unsigned int, seqan::Alloc<void> >' requested here
        uint32_t slen = (uint32_t)seqan::length(bucket);
                                  ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:9: warning: implicit conversion changes signedness: 'typename Difference<Iter<const String<SimpleType<unsigned char, _Dna>, Packed<Alloc<void> > >, Packed<Alloc<void> > > >::Type' (aka 'long') to 'typename Size<const String<SimpleType<unsigned char, _Dna>, Packed<Alloc<void> > > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./blockwise_sa.h:354:27: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >' requested here
        uint32_t len = (uint32_t)seqan::length(t);
                                 ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:431:23: warning: implicit conversion changes signedness: 'int' to 'TPosition' (aka 'unsigned long') [-Wsign-conversion]
        return TIterator(me, pos_);
               ˜˜˜˜˜˜˜˜˜     ^˜˜˜
SeqAn-1.1/seqan/sequence/string_packed.h:450:9: note: in instantiation of function template specialization 'seqan::iter<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, int, seqan::TagStandard_>' requested here
        return iter(me, 0, tag_);
               ^
SeqAn-1.1/seqan/sequence/string_base.h:181:31: note: in instantiation of function template specialization 'seqan::begin<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, seqan::TagStandard_>' requested here
        return end(me, Standard()) - begin(me, Standard());
                                     ^
./blockwise_sa.h:354:27: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >' requested here
        uint32_t len = (uint32_t)seqan::length(t);
                                 ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:1237:24: warning: implicit conversion changes signedness: 'unsigned long' to 'typename Difference<Iter<const String<SimpleType<unsigned char, _Dna>, Packed<Alloc<void> > >, Packed<Alloc<void> > > >::Type' (aka 'long') [-Wsign-conversion]
        return position(left) - position(right);
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:181:29: note: in instantiation of function template specialization 'seqan::operator-<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void> >' requested here
        return end(me, Standard()) - begin(me, Standard());
                                   ^
./blockwise_sa.h:354:27: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >' requested here
        uint32_t len = (uint32_t)seqan::length(t);
                                 ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:906:88: warning: implicit conversion changes signedness: 'long' to 'typename Position<const Iter<const String<SimpleType<unsigned char, _Dna>, Packed<Alloc<void> > >, Packed<Alloc<void> > > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return (hostIterator(me) - begin(host_)) * _PackedConsts<TContainer>::VALUES_PER_WORD + _bitpos(me) / _PackedConsts<TContainer>::BITS_PER_VALUE;
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_packed.h:1237:9: note: in instantiation of function template specialization 'seqan::position<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void> >' requested here
        return position(left) - position(right);
               ^
SeqAn-1.1/seqan/sequence/string_base.h:181:29: note: in instantiation of function template specialization 'seqan::operator-<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void> >' requested here
        return end(me, Standard()) - begin(me, Standard());
                                   ^
./blockwise_sa.h:354:27: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >' requested here
        uint32_t len = (uint32_t)seqan::length(t);
                                 ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:360:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                mkeyQSortSufDcU8(t, t, len, s, slen, *_dc,
                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1079:10: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1098:30: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1108:30: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1064:65: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                       ^˜˜˜˜
./multikey_qsort.h:1064:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                              ^˜˜
./multikey_qsort.h:1073:65: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                       ^˜˜˜˜
./multikey_qsort.h:1073:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                              ^˜˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1079:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1079:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1079:32: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1098:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1098:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1098:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1108:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1108:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1108:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:748:14: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        size_t a = (rand() % n) + begin; // choose pivot between begin and end
                    ^˜˜˜˜˜ ˜
./multikey_qsort.h:1062:3: note: in instantiation of function template specialization 'qsortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                qsortSufDcU8<T1,T2>(seqanHost, host, hlen, s, slen, dc, begin, end, sanityCheck);
                ^
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:360:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                mkeyQSortSufDcU8(t, t, len, s, slen, *_dc,
                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:977:39: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                               0xffffffff, begin, end);
                                                           ^˜˜˜˜
./multikey_qsort.h:1070:3: note: in instantiation of function template specialization 'bucketSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                bucketSortSufDcU8(seqanHost, host, hlen, s, slen, dc,
                ^
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:360:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                mkeyQSortSufDcU8(t, t, len, s, slen, *_dc,
                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:977:46: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                               0xffffffff, begin, end);
                                                                  ^˜˜
./multikey_qsort.h:982:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t off = depth+s[i];
                         ˜˜˜   ˜˜˜˜˜^˜˜˜˜
./multikey_qsort.h:992:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t cur = begin + cnts[0];
                 ˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./multikey_qsort.h:1000:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cur = begin;
            ˜ ^˜˜˜˜
./multikey_qsort.h:852:41: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                               0xffffffff, begin, end);
                                                                           ^˜˜˜˜
./multikey_qsort.h:973:3: note: in instantiation of function template specialization 'selectionSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                selectionSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi,
                ^
./multikey_qsort.h:1070:3: note: in instantiation of function template specialization 'bucketSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                bucketSortSufDcU8(seqanHost, host, hlen, s, slen, dc,
                ^
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:360:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                mkeyQSortSufDcU8(t, t, len, s, slen, *_dc,
                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:852:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                               0xffffffff, begin, end);
                                                                                  ^˜˜
./multikey_qsort.h:856:20: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        v = off - depth + 1;
                          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./multikey_qsort.h:863:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t targ = i;
                         ˜˜˜˜   ^
./multikey_qsort.h:864:28: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t targoff = depth + s[i];
                         ˜˜˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:867:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        uint32_t joff = depth + s[j];
                                 ˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:883:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        targ = j;
                                             ˜ ^
./multikey_qsort.h:899:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                targ = j;
                                                     ˜ ^
./multikey_qsort.h:916:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        targ = j;
                                             ˜ ^
./multikey_qsort.h:937:38: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                       0xffffffff, begin, end);
                                                   ^˜˜˜˜
./multikey_qsort.h:937:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                       0xffffffff, begin, end);
                                                          ^˜˜
./multikey_qsort.h:326:35: warning: implicit conversion loses integer precision: 'unsigned long' to 'const unsigned int' [-Wshorten-64-to-32]
        upper = min<uint32_t>(upper, slen-1);
                ˜˜˜                  ˜˜˜˜^˜
./multikey_qsort.h:688:18: note: in instantiation of function template specialization 'sanityCheckOrderedSufs<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
        if(sanityCheck) sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff);
                        ^
./blockwise_sa.h:360:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                mkeyQSortSufDcU8(t, t, len, s, slen, *_dc,
                ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:415:50: warning: implicit conversion changes signedness: 'int' to 'typename Size<String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        if (old_capacity >= (TSize)new_capacity) return new_capacity;
                                                 ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/sequence_interface.h:1325:9: note: in instantiation of function template specialization 'seqan::reserve<QueryMutation, void, int, seqan::TagExact_>' requested here
        return reserve(me, new_capacity, typename DefaultOverflowExplicit<T>::Type());
               ^
./ebwt_search_util.h:315:3: note: in instantiation of function template specialization 'seqan::reserve<seqan::String<QueryMutation, seqan::Alloc<void> >, int>' requested here
                reserve(muts, 4);
                ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:418:94: warning: implicit conversion changes signedness: 'int' to 'typename Size<String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        typename Value< String<TValue, Alloc<TSpec> > >::Type * old_array = _reallocateStorage(seq, new_capacity, tag);
                                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_alloc.h:430:9: warning: implicit conversion changes signedness: 'int' to 'typename Size<String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return new_capacity;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:11:
./ebwt.h:2091:59: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
        if(l._sideByteOff <= _zEbwtByteOff && l._sideByteOff + l._by >= _zEbwtByteOff) {
                                                             ˜ ˜˜^˜˜
./ebwt.h:2243:15: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countFwSideEx' requested here
        if(ltop._fw) countFwSideEx(ltop, tops); // Forward side
                     ^
./ebwt_search_backtrack.h:552:10: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::mapLFEx' requested here
                                ebwt.mapLFEx(ltop, lbot, &pairs[d*8], &pairs[(d*8)+4]);
                                     ^
In file included from ebwt_build.cpp:11:
./ebwt.h:2094:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                if((l._sideByteOff + l._by > _zEbwtByteOff) ||
                                   ˜ ˜˜^˜˜
./ebwt.h:2095:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                   (l._sideByteOff + l._by == _zEbwtByteOff && l._bp > _zEbwtBpOff))
                                   ˜ ˜˜^˜˜
./ebwt.h:2190:59: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
        if(l._sideByteOff <= _zEbwtByteOff && l._sideByteOff + l._by >= _zEbwtByteOff) {
                                                             ˜ ˜˜^˜˜
./ebwt.h:2244:15: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countBwSideEx' requested here
        else         countBwSideEx(ltop, tops); // Backward side
                     ^
./ebwt_search_backtrack.h:552:10: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::mapLFEx' requested here
                                ebwt.mapLFEx(ltop, lbot, &pairs[d*8], &pairs[(d*8)+4]);
                                     ^
In file included from ebwt_build.cpp:11:
./ebwt.h:2193:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                if((l._sideByteOff + l._by > _zEbwtByteOff) ||
                                   ˜ ˜˜^˜˜
./ebwt.h:2194:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                   (l._sideByteOff + l._by == _zEbwtByteOff && l._bp >= _zEbwtBpOff))
                                   ˜ ˜˜^˜˜
./ebwt.h:2035:69: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
        if(c == 0 && l._sideByteOff <= _zEbwtByteOff && l._sideByteOff + l._by >= _zEbwtByteOff) {
                                                                       ˜ ˜˜^˜˜
./ebwt.h:2374:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countFwSide' requested here
        if(l._fw) ret = countFwSide(l, c); // Forward side
                        ^
./ebwt_search_backtrack.h:565:24: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::mapLF1' requested here
                                                bot = top = ebwt.mapLF1(top, ltop, c);
                                                                 ^
In file included from ebwt_build.cpp:11:
./ebwt.h:2038:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                if((l._sideByteOff + l._by > _zEbwtByteOff) ||
                                   ˜ ˜˜^˜˜
./ebwt.h:2039:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                   (l._sideByteOff + l._by == _zEbwtByteOff && l._bp > _zEbwtBpOff))
                                   ˜ ˜˜^˜˜
./ebwt.h:1945:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                cCnt += countInU64(c, *(uint64_t*)&side[i]);
                     ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:2033:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countUpTo' requested here
        uint32_t cCnt = countUpTo(l, c);
                        ^
./ebwt.h:2374:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countFwSide' requested here
        if(l._fw) ret = countFwSide(l, c); // Forward side
                        ^
./ebwt_search_backtrack.h:565:24: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::mapLF1' requested here
                                                bot = top = ebwt.mapLF1(top, ltop, c);
                                                                 ^
In file included from ebwt_build.cpp:11:
./ebwt.h:2140:69: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
        if(c == 0 && l._sideByteOff <= _zEbwtByteOff && l._sideByteOff + l._by >= _zEbwtByteOff) {
                                                                       ˜ ˜˜^˜˜
./ebwt.h:2375:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countBwSide' requested here
        else      ret = countBwSide(l, c); // Backward side
                        ^
./ebwt_search_backtrack.h:565:24: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::mapLF1' requested here
                                                bot = top = ebwt.mapLF1(top, ltop, c);
                                                                 ^
In file included from ebwt_build.cpp:11:
./ebwt.h:2143:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                if((l._sideByteOff + l._by > _zEbwtByteOff) ||
                                   ˜ ˜˜^˜˜
./ebwt.h:2144:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                   (l._sideByteOff + l._by == _zEbwtByteOff && l._bp >= _zEbwtBpOff))
                                   ˜ ˜˜^˜˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1377:25: note: in instantiation of function template specialization 'seqan::length<QueryMutation, seqan::Alloc<void> >' requested here
                for(size_t i = 0; i < length(*_muts); i++) {
                                      ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:323:17: warning: implicit conversion loses integer precision: 'const int' to 'unsigned char' [-Wconversion]
        target.value = source;
                     ˜ ^˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:82:3: note: in instantiation of function template specialization 'seqan::assign<unsigned char, seqan::_Dna5, int>' requested here
                assign(*this, other);
                ^
./ebwt_search_backtrack.h:1384:21: note: in instantiation of function template specialization 'seqan::SimpleType<unsigned char, seqan::_Dna5>::SimpleType<int>' requested here
                        (*_qry)[m.pos] = (Dna5)(int)m.newBase; // apply it
                                         ^
In file included from ebwt_build.cpp:11:
./ebwt.h:2597:37: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
        const uint32_t offRate = this->_eh._offRate;
                       ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1550:14: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reportChaseOne' requested here
                        if(_ebwt->reportChaseOne((*_qry), _qual, _name,
                                  ^
In file included from ebwt_build.cpp:11:
./ebwt.h:1285:17: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                hit.stratum = stratum;
                            ˜ ^˜˜˜˜˜˜
./ebwt.h:2528:16: note: in instantiation of member function 'EbwtSearchParams<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reportHit' requested here
        return params.reportHit(
                      ^
./ebwt.h:2634:9: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::report' requested here
        return report(query, quals, name, color, primer, trimc, colExEnds,
               ^
./ebwt_search_backtrack.h:1550:14: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reportChaseOne' requested here
                        if(_ebwt->reportChaseOne((*_qry), _qual, _name,
                                  ^
In file included from ebwt_build.cpp:11:
./ebwt.h:1307:24: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.crefcs[off] = refcs[i];
                                                        ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1310:22: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.crefcs[i] = refcs[i];
                                                      ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1331:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        read[i] = (int)hit.patSeq[i];
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1332:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                        qual[i] = mmPenalty(maqRound, phredCharToPhredQual(hit.quals[i]));
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1340:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                rf[i] = (1 << rf[i]);
                                      ˜  ˜˜^˜˜˜˜˜˜˜
./ebwt.h:1356:39: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        size_t nqlen = qlen + (colExEnds ? -1 : 1);
                                            ˜              ^˜
./ebwt.h:1427:23: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.refcs[off] = refcs[i];
                                                       ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1430:29: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.refcs[mmui32[i]] = refcs[i];
                                                             ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1397:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        uint32_t off = i - (colExEnds? 1:0);
                                                 ˜˜˜   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1398:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        if(!_fw) off = nqlen - off - 1;
                                                     ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:1401:60: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        hit.refcs[off] = "ACGT"[ref->getBase(h.first, h.second+i)];
                                                                ˜˜˜                   ˜˜˜˜˜˜˜˜^˜
./ebwt.h:1447:22: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        uint32_t qoff = i;
                                                 ˜˜˜˜   ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:31:
In file included from ./hit.h:15:
./bitset.h:386:17: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        oss << (test(i)? "1" : "0");
                                ˜˜˜˜ ^
./ebwt.h:1459:36: note: in instantiation of member function 'FixedBitset<1024>::str' requested here
                                cerr << "Expected " << hit.mms.str() << " mismatches, got " << diffs.str() << endl;
                                                               ^
./ebwt.h:2528:16: note: in instantiation of member function 'EbwtSearchParams<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reportHit' requested here
        return params.reportHit(
                      ^
./ebwt.h:2634:9: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::report' requested here
        return report(query, quals, name, color, primer, trimc, colExEnds,
               ^
./ebwt_search_backtrack.h:1550:14: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reportChaseOne' requested here
                        if(_ebwt->reportChaseOne((*_qry), _qual, _name,
                                  ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:1607:
In file included from ./ebwt_search_backtrack.h:10:
./range_source.h:1699:54: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                foundRange(false), done(_done), minCostAdjustment_(minCostAdjustment)
                                                                  ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:3010:4: note: in instantiation of member function 'RangeSourceDriver<EbwtRangeSource>::RangeSourceDriver' requested here
                        RangeSourceDriver<EbwtRangeSource>(true, 0),
                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:1607:
In file included from ./ebwt_search_backtrack.h:10:
./range_source.h:2467:29: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                                vec.erase(vec.begin() + i);
                                          ˜˜˜           ^
./range_source.h:2200:3: note: in instantiation of member function 'CostAwareRangeSourceDriver<EbwtRangeSource>::sortActives' requested here
                sortActives();
                ^
./ebwt_search_backtrack.h:3127:13: note: in instantiation of member function 'CostAwareRangeSourceDriver<EbwtRangeSource>::addSource' requested here
                                rsFull_.addSource(partial, seedRange_);
                                        ^
ebwt_build.cpp:174:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                return t;
                ˜˜˜˜˜˜ ^
ebwt_build.cpp:222:12: note: in instantiation of function template specialization 'parseNumber<unsigned int>' requested here
                                bmax = parseNumber<uint32_t>(1, "--bmax arg must be at least 1");
                                       ^
ebwt_build.cpp:429:18: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seed,         // pseudo-random number generator seed
                        ^˜˜˜
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
ebwt_build.cpp:458:5: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                seed);       // pseudo-random number generator seed
                                ^˜˜˜
ebwt_build.cpp:345:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                writeU32(fout3, szs.size(), bigEndian); // write # records
                                ˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜
ebwt_build.cpp:359:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                writeU32(fout3, szs.size(), bigEndian); // write # records
                                ˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜
ebwt_build.cpp:427:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sztot.first,  // total size of all unambiguous ref chars
                        ˜˜˜˜˜˜^˜˜˜˜
ebwt_build.cpp:456:11: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                sztot.first, // total size of all unambiguous ref chars
                                ˜˜˜˜˜˜^˜˜˜˜
In file included from ebwt_build.cpp:11:
./ebwt.h:702:69: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        size_t sz = DifferenceCoverSample<TStr>::simulateAllocs(s, dcv >> 1);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                          ˜˜˜˜^˜˜˜
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
./ebwt.h:723:46: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ˜˜˜          ^˜˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
./ebwt.h:597:4: note: in instantiation of function template specialization 'seqan::reserve<seqan::SimpleType<unsigned char, seqan::_Dna>, void, unsigned int, seqan::TagExact_>' requested here
                        seqan::reserve(s, jlen, Exact());
                        ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:32:
./ref_read.h:173:31: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                if (name) name->push_back(c);
                                          ˜˜˜˜            ^
./ebwt.h:4011:20: note: in instantiation of function template specialization 'fastaRefReadAppend<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                        RefRecord rec = fastaRefReadAppend(*l[i], first, ret, rpcp, &_refnames.back());
                                        ^
./ebwt.h:602:6: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::joinToDisk' requested here
                                        joinToDisk(is, szs, plens, sztot, refparams, s, out1, out2, seed);
                                        ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:32:
./ref_read.h:282:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return RefRecord(off, len, first);
               ˜˜˜˜˜˜˜˜˜ ^˜˜
./ref_read.h:282:24: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return RefRecord(off, len, first);
               ˜˜˜˜˜˜˜˜˜      ^˜˜
In file included from ebwt_build.cpp:11:
./ebwt.h:555:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        writeU32(os, seqm1,  this->toBe()); // sequence id
                        ˜˜˜˜˜˜˜˜     ^˜˜˜˜
./ebwt.h:608:6: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::szsToDisk' requested here
                                        szsToDisk(tmp, out1, refparams.reverse);
                                        ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
./ebwt.h:556:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        writeU32(os, fwoff,  this->toBe()); // offset into sequence
                        ˜˜˜˜˜˜˜˜     ^˜˜˜˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<unsigned int>' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<unsigned int>' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<unsigned int>' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_base.h:764:4: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<unsigned int>' requested here
                        arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
                        ^
SeqAn-1.1/seqan/sequence/string_base.h:812:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<unsigned int, seqan::Alloc<void> >, const seqan::String<unsigned int, seqan::Alloc<void> > >' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:737:2: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
        ^
./diff_sample.h:545:25: note: in instantiation of function template specialization 'getDiffCover<unsigned int>' requested here
                String<uint32_t> ds = getDiffCover(v, false /*verbose*/, false /*sanity*/);
                                      ^
./ebwt.h:702:47: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::simulateAllocs' requested here
                                        size_t sz = DifferenceCoverSample<TStr>::simulateAllocs(s, dcv >> 1);
                                                                                 ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:275:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:294:2: note: in instantiation of function template specialization 'seqan::_arrayMoveForward_Pointer<unsigned int>' requested here
        _arrayMoveForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:136:2: note: in instantiation of function template specialization 'seqan::arrayMoveForward<unsigned int>' requested here
        arrayMoveForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:155:2: note: in instantiation of function template specialization 'seqan::_arrayConstructMove_Pointer<unsigned int>' requested here
        _arrayConstructMove_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_base.h:487:4: note: in instantiation of function template specialization 'seqan::arrayConstructMove<unsigned int>' requested here
                        arrayConstructMove(old_array, old_array + start, seq_array);
                        ^
SeqAn-1.1/seqan/sequence/string_base.h:656:9: note: in instantiation of function template specialization 'seqan::_ClearSpace_Expand_String_Base_<const seqan::Tag<seqan::TagGenerous_> >::_clearSpace_<seqan::String<unsigned int, seqan::Alloc<void> > >' requested here
        return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end);
               ^
SeqAn-1.1/seqan/sequence/string_base.h:987:47: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                        typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand());
                                                                   ^
./diff_sample.h:545:25: note: in instantiation of function template specialization 'getDiffCover<unsigned int>' requested here
                String<uint32_t> ds = getDiffCover(v, false /*verbose*/, false /*sanity*/);
                                      ^
./ebwt.h:702:47: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::simulateAllocs' requested here
                                        size_t sz = DifferenceCoverSample<TStr>::simulateAllocs(s, dcv >> 1);
                                                                                 ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:309:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:328:2: note: in instantiation of function template specialization 'seqan::_arrayMoveBackward_Pointer<unsigned int>' requested here
        _arrayMoveBackward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_interface.h:741:3: note: in instantiation of function template specialization 'seqan::arrayMoveBackward<unsigned int>' requested here
                arrayMoveBackward(source_begin, source_end, target_begin);
                ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:345:2: note: in instantiation of function template specialization 'seqan::arrayMove<unsigned int *, unsigned int *, unsigned int *>' requested here
        arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:363:2: note: in instantiation of function template specialization 'seqan::_arrayClearSpace_Pointer<unsigned int>' requested here
        _arrayClearSpace_Pointer(array_begin, array_length, keep_from, move_to, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_base.h:494:4: note: in instantiation of function template specialization 'seqan::arrayClearSpace<unsigned int>' requested here
                        arrayClearSpace(seq_array + start, old_length - start, removed_size, size);
                        ^
SeqAn-1.1/seqan/sequence/string_base.h:656:9: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end);
               ^
./diff_sample.h:545:25: note: in instantiation of function template specialization 'getDiffCover<unsigned int>' requested here
                String<uint32_t> ds = getDiffCover(v, false /*verbose*/, false /*sanity*/);
                                      ^
./ebwt.h:702:47: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::simulateAllocs' requested here
                                        size_t sz = DifferenceCoverSample<TStr>::simulateAllocs(s, dcv >> 1);
                                                                                 ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:100:
SeqAn-1.1/seqan/basic/basic_alphabet_interface.h:96:29: warning: implicit conversion changes signedness: 'const int' to 'TValue' (aka 'unsigned int') [-Wsign-conversion]
                new( & value(it) ) TValue(param_);
                ˜˜˜                       ^˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_interface.h:178:2: note: in instantiation of function template specialization 'seqan::_ValueConstructor::construct<unsigned int *, int>' requested here
        TConstructor::construct(it, param_);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_interface.h:353:3: note: in instantiation of function template specialization 'seqan::valueConstruct<unsigned int *, int>' requested here
                valueConstruct(target_begin, *source_begin);
                ^
SeqAn-1.1/seqan/basic/basic_alphabet_interface.h:366:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Default<unsigned int *, const int *, const int *>' requested here
        _arrayConstructCopy_Default(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:988:4: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<unsigned int *, const int *, const int *>' requested here
                        arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()) + target_length);
                        ^
SeqAn-1.1/seqan/sequence/string_base.h:1045:2: note: in instantiation of function template specialization 'seqan::_Append_String<const seqan::Tag<seqan::TagGenerous_> >::append_<seqan::String<unsigned int, seqan::Alloc<void> >, const int>' requested here
        _Append_String<Tag<TExpand> const>::append_(target, source);
        ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1043:2: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        append(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
        ^
./diff_sample.h:545:25: note: in instantiation of function template specialization 'getDiffCover<unsigned int>' requested here
                String<uint32_t> ds = getDiffCover(v, false /*verbose*/, false /*sanity*/);
                                      ^
./ebwt.h:702:47: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::simulateAllocs' requested here
                                        size_t sz = DifferenceCoverSample<TStr>::simulateAllocs(s, dcv >> 1);
                                                                                 ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<int, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:763:67: note: in instantiation of function template specialization 'seqan::length<int, seqan::Alloc<void> >' requested here
                        typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), TExpand());
                                                                                       ^
SeqAn-1.1/seqan/sequence/string_base.h:812:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<int, seqan::Alloc<void> >, const seqan::String<int, seqan::Alloc<void> > >' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:798:4: note: in instantiation of function template specialization 'seqan::assign<int, seqan::Alloc<void>, seqan::String<int, seqan::Alloc<void> >, seqan::TagGenerous_>' requested here
                        assign(target, temp, TExpand());
                        ^
SeqAn-1.1/seqan/sequence/string_base.h:822:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<int, seqan::Alloc<void> >, const int>' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source, limit);
        ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:990:2: note: in instantiation of function template specialization 'seqan::assign<int, seqan::Alloc<void>, int, unsigned long, seqan::TagGenerous_>' requested here
        assign(target, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:113:3: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                assign(*this, source, limit);
                ^
./diff_sample.h:545:25: note: in instantiation of function template specialization 'getDiffCover<unsigned int>' requested here
                String<uint32_t> ds = getDiffCover(v, false /*verbose*/, false /*sanity*/);
                                      ^
./ebwt.h:702:47: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::simulateAllocs' requested here
                                        size_t sz = DifferenceCoverSample<TStr>::simulateAllocs(s, dcv >> 1);
                                                                                 ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<int>' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<int>' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<int>' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_base.h:764:4: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<int>' requested here
                        arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
                        ^
SeqAn-1.1/seqan/sequence/string_base.h:812:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<int, seqan::Alloc<void> >, const seqan::String<int, seqan::Alloc<void> > >' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:798:4: note: (skipping 8 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                        assign(target, temp, TExpand());
                        ^
./diff_sample.h:545:25: note: in instantiation of function template specialization 'getDiffCover<unsigned int>' requested here
                String<uint32_t> ds = getDiffCover(v, false /*verbose*/, false /*sanity*/);
                                      ^
./ebwt.h:702:47: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::simulateAllocs' requested here
                                        size_t sz = DifferenceCoverSample<TStr>::simulateAllocs(s, dcv >> 1);
                                                                                 ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
./ebwt.h:4193:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        int sideCur = eh._sideBwtSz - 1;
            ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:727:5: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::buildToDisk' requested here
                                buildToDisk(bsa, s, out1, out2);
                                ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
./ebwt.h:4266:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                sufInt |= (unsigned char)(Dna)(s[saElt+i]);
                                                                                      ˜^
./ebwt.h:4354:28: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        sideCur = eh._sideBwtSz - 1;
                                ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:4437:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        eftabLen = eh._ftabChars*2;
                 ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:523:6: warning: implicit conversion loses integer precision: 'typename Size<const String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                _d(length(_ds)),
                  ˜^˜˜˜˜˜˜˜˜˜˜
./blockwise_sa.h:268:14: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::DifferenceCoverSample' requested here
                        _dc = new TDC(this->text(), _dcV, this->verbose(), this->sanityCheck());
                                  ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:535:59: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'typename Value<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned int') [-Wshorten-64-to-32]
                for(size_t i = 0; i < length(_ds); i++) _dInv[_ds[i]] = i;
                                                                      ˜ ^
./diff_sample.h:498:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
                if(i & 1) return j;
                          ˜˜˜˜˜˜ ^
./diff_sample.h:527:10: note: in instantiation of function template specialization 'myLog2<unsigned int>' requested here
                _log2v(myLog2(_v)),
                       ^
./blockwise_sa.h:268:14: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::DifferenceCoverSample' requested here
                        _dc = new TDC(this->text(), _dcV, this->verbose(), this->sanityCheck());
                                  ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:1510:9: warning: implicit conversion loses integer precision: 'typename Size<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
        return _Fill_String<Tag<TExpand> const>::fill_(me, new_length, val);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./diff_sample.h:534:3: note: in instantiation of function template specialization 'seqan::fill<unsigned int, seqan::Alloc<void>, unsigned int, unsigned int, seqan::TagExact_>' requested here
                fill(_dInv, _v, 0xffffffff, Exact());
                ^
./blockwise_sa.h:268:14: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::DifferenceCoverSample' requested here
                        _dc = new TDC(this->text(), _dcV, this->verbose(), this->sanityCheck());
                                  ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:783:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'typename Value<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sPrimeOrder[i] = i;
                                       ˜ ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:851:59: warning: implicit conversion loses integer precision: 'typename Size<const String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
                createSuffixArray(sPrime, _isaPrime, LarssonSadakane(), length(_isaPrime));
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./diff_sample.h:684:18: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t tlen = length(t);
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜
./diff_sample.h:773:2: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::buildSPrime' requested here
        buildSPrime(sPrime);
        ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:326:35: warning: implicit conversion loses integer precision: 'unsigned long' to 'const unsigned int' [-Wshorten-64-to-32]
        upper = min<uint32_t>(upper, slen-1);
                ˜˜˜                  ˜˜˜˜^˜
./multikey_qsort.h:590:3: note: in instantiation of function template specialization 'sanityCheckOrderedSufs<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                sanityCheckOrderedSufs(host, hlen, s, slen, upto);
                ^
./diff_sample.h:807:4: note: in instantiation of function template specialization 'mkeyQSortSuf2<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                        mkeyQSortSuf2(t, sPrimeArr, slen, sPrimeOrderArr,
                        ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:100:
SeqAn-1.1/seqan/basic/basic_alphabet_interface.h:96:29: warning: implicit conversion loses integer precision: 'const unsigned long' to 'TValue' (aka 'unsigned int') [-Wshorten-64-to-32]
                new( & value(it) ) TValue(param_);
                ˜˜˜                       ^˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_interface.h:178:2: note: in instantiation of function template specialization 'seqan::_ValueConstructor::construct<unsigned int *, unsigned long>' requested here
        TConstructor::construct(it, param_);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_interface.h:353:3: note: in instantiation of function template specialization 'seqan::valueConstruct<unsigned int *, unsigned long>' requested here
                valueConstruct(target_begin, *source_begin);
                ^
SeqAn-1.1/seqan/basic/basic_alphabet_interface.h:366:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Default<unsigned int *, const unsigned long *, const unsigned long *>' requested here
        _arrayConstructCopy_Default(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:988:4: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<unsigned int *, const unsigned long *, const unsigned long *>' requested here
                        arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()) + target_length);
                        ^
SeqAn-1.1/seqan/sequence/string_base.h:1045:2: note: in instantiation of function template specialization 'seqan::_Append_String<const seqan::Tag<seqan::TagGenerous_> >::append_<seqan::String<unsigned int, seqan::Alloc<void> >, const unsigned long>' requested here
        _Append_String<Tag<TExpand> const>::append_(target, source);
        ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1043:2: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        append(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
        ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<unsigned long, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:763:67: note: in instantiation of function template specialization 'seqan::length<unsigned long, seqan::Alloc<void> >' requested here
                        typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), TExpand());
                                                                                       ^
SeqAn-1.1/seqan/sequence/string_base.h:812:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<unsigned long, seqan::Alloc<void> >, const seqan::String<unsigned long, seqan::Alloc<void> > >' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:798:4: note: in instantiation of function template specialization 'seqan::assign<unsigned long, seqan::Alloc<void>, seqan::String<unsigned long, seqan::Alloc<void> >, seqan::TagGenerous_>' requested here
                        assign(target, temp, TExpand());
                        ^
SeqAn-1.1/seqan/sequence/string_base.h:822:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<unsigned long, seqan::Alloc<void> >, const unsigned long>' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source, limit);
        ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:990:2: note: in instantiation of function template specialization 'seqan::assign<unsigned long, seqan::Alloc<void>, unsigned long, unsigned long, seqan::TagGenerous_>' requested here
        assign(target, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:113:3: note: (skipping 6 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                assign(*this, source, limit);
                ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<unsigned long>' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<unsigned long>' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<unsigned long>' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_base.h:764:4: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<unsigned long>' requested here
                        arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
                        ^
SeqAn-1.1/seqan/sequence/string_base.h:812:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<unsigned long, seqan::Alloc<void> >, const seqan::String<unsigned long, seqan::Alloc<void> > >' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:798:4: note: (skipping 9 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                        assign(target, temp, TExpand());
                        ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:62:
SeqAn-1.1/seqan/index/index_sa_lss.h:360:4: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        K,                                                                      // text[i] <  K
                        ^
./diff_sample.h:851:3: note: in instantiation of function template specialization 'seqan::createSuffixArray<seqan::String<unsigned int, seqan::Alloc<void> >, seqan::String<unsigned int, seqan::Alloc<void> > >' requested here
                createSuffixArray(sPrime, _isaPrime, LarssonSadakane(), length(_isaPrime));
                ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:62:
SeqAn-1.1/seqan/index/index_sa_lss.h:359:14: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                        length(s) - 1,                                          // n
                        ˜˜˜˜˜˜˜˜˜˜^˜˜
SeqAn-1.1/seqan/index/index_sa_lss.h:317:22: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                sort_split(pi, pk-pi);
                                ˜˜˜˜˜˜˜˜˜˜     ˜˜^˜˜
SeqAn-1.1/seqan/index/index_sa_lss.h:356:5: note: in instantiation of member function 'seqan::_Context_LSS<int>::suffixsort' requested here
                c.suffixsort(
                  ^
./diff_sample.h:851:3: note: in instantiation of function template specialization 'seqan::createSuffixArray<seqan::String<unsigned int, seqan::Alloc<void> >, seqan::String<unsigned int, seqan::Alloc<void> > >' requested here
                createSuffixArray(sPrime, _isaPrime, LarssonSadakane(), length(_isaPrime));
                ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:62:
SeqAn-1.1/seqan/index/index_sa_lss.h:160:14: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
           if ((s=pa-p)>(t=pb-pa))
                 ˜˜˜^˜
SeqAn-1.1/seqan/index/index_sa_lss.h:300:5: note: in instantiation of member function 'seqan::_Context_LSS<int>::sort_split' requested here
                  sort_split(I, n+1);       /* quicksort on first r positions.*/
                  ^
SeqAn-1.1/seqan/index/index_sa_lss.h:356:5: note: in instantiation of member function 'seqan::_Context_LSS<int>::suffixsort' requested here
                c.suffixsort(
                  ^
./diff_sample.h:851:3: note: in instantiation of function template specialization 'seqan::createSuffixArray<seqan::String<unsigned int, seqan::Alloc<void> >, seqan::String<unsigned int, seqan::Alloc<void> > >' requested here
                createSuffixArray(sPrime, _isaPrime, LarssonSadakane(), length(_isaPrime));
                ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:62:
SeqAn-1.1/seqan/index/index_sa_lss.h:160:23: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
           if ((s=pa-p)>(t=pb-pa))
                          ˜˜˜^˜˜
SeqAn-1.1/seqan/index/index_sa_lss.h:164:14: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
           if ((s=pd-pc)>(t=pn-pd-1))
                 ˜˜˜^˜˜
SeqAn-1.1/seqan/index/index_sa_lss.h:164:27: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
           if ((s=pd-pc)>(t=pn-pd-1))
                           ˜˜˜˜˜˜^˜
SeqAn-1.1/seqan/index/index_sa_lss.h:169:9: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
           s=pb-pa;
            ˜˜˜^˜˜
SeqAn-1.1/seqan/index/index_sa_lss.h:170:9: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
           t=pd-pc;
            ˜˜˜^˜˜
SeqAn-1.1/seqan/index/index_sa_lss.h:93:14: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                  V[*pa]=pa-I;
                        ˜˜˜^˜
SeqAn-1.1/seqan/index/index_sa_lss.h:131:5: note: in instantiation of member function 'seqan::_Context_LSS<int>::select_sort_split' requested here
                  select_sort_split(p, n);
                  ^
SeqAn-1.1/seqan/index/index_sa_lss.h:300:5: note: in instantiation of member function 'seqan::_Context_LSS<int>::sort_split' requested here
                  sort_split(I, n+1);       /* quicksort on first r positions.*/
                  ^
SeqAn-1.1/seqan/index/index_sa_lss.h:356:5: note: in instantiation of member function 'seqan::_Context_LSS<int>::suffixsort' requested here
                c.suffixsort(
                  ^
./diff_sample.h:851:3: note: in instantiation of function template specialization 'seqan::createSuffixArray<seqan::String<unsigned int, seqan::Alloc<void> >, seqan::String<unsigned int, seqan::Alloc<void> > >' requested here
                createSuffixArray(sPrime, _isaPrime, LarssonSadakane(), length(_isaPrime));
                ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:62:
SeqAn-1.1/seqan/index/index_sa_lss.h:60:9: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
           g=pm-I;                      /* group number.*/
            ˜˜˜^˜
SeqAn-1.1/seqan/index/index_sa_lss.h:173:5: note: in instantiation of member function 'seqan::_Context_LSS<int>::update_group' requested here
           update_group(p+s, p+n-t-1);
           ^
SeqAn-1.1/seqan/index/index_sa_lss.h:300:5: note: in instantiation of member function 'seqan::_Context_LSS<int>::sort_split' requested here
                  sort_split(I, n+1);       /* quicksort on first r positions.*/
                  ^
SeqAn-1.1/seqan/index/index_sa_lss.h:356:5: note: in instantiation of member function 'seqan::_Context_LSS<int>::suffixsort' requested here
                c.suffixsort(
                  ^
./diff_sample.h:851:3: note: in instantiation of function template specialization 'seqan::createSuffixArray<seqan::String<unsigned int, seqan::Alloc<void> >, seqan::String<unsigned int, seqan::Alloc<void> > >' requested here
                createSuffixArray(sPrime, _isaPrime, LarssonSadakane(), length(_isaPrime));
                ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:662:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'typename Value<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sorted[_isaPrime[doi]] = v*i + d;
                                               ˜ ˜˜˜˜^˜˜
./diff_sample.h:867:26: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::doBuiltSanityCheck' requested here
        if(this->sanityCheck()) doBuiltSanityCheck();
                                ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:383:17: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t len = length(this->text());
                 ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./blockwise_sa.h:274:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::buildSamples' requested here
                        buildSamples();
                        ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:445:45: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t numBuckets = length(_sampleSuffs)+1;
                         ˜˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:37:
SeqAn-1.1/seqan/sequence/sequence_interface.h:1395:25: warning: implicit conversion changes signedness: 'int' to 'typename Size<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit<T>::Type());
               ˜˜˜˜˜˜˜˜˜˜˜     ^˜˜˜
SeqAn-1.1/seqan/sequence/sequence_interface.h:1444:2: note: in instantiation of function template specialization 'seqan::resizeSpace<seqan::String<unsigned int, seqan::Alloc<void> >, int, unsigned long>' requested here
        resizeSpace(me, 0, pos, pos + 1);
        ^
./blockwise_sa.h:427:5: note: in instantiation of function template specialization 'seqan::erase<seqan::String<unsigned int, seqan::Alloc<void> >, unsigned long>' requested here
                                erase(_sampleSuffs, i--);
                                ^
./blockwise_sa.h:274:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::buildSamples' requested here
                        buildSamples();
                        ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:37:
SeqAn-1.1/seqan/sequence/sequence_interface.h:1395:9: warning: implicit conversion loses integer precision: 'typename Size<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit<T>::Type());
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:1510:9: warning: implicit conversion loses integer precision: 'typename Size<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
        return _Fill_String<Tag<TExpand> const>::fill_(me, new_length, val);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./blockwise_sa.h:451:4: note: in instantiation of function template specialization 'seqan::fill<unsigned int, seqan::Alloc<void>, unsigned int, int, seqan::TagExact_>' requested here
                        fill(bucketSzs, numBuckets, 0, Exact());
                        ^
./blockwise_sa.h:274:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::buildSamples' requested here
                        buildSamples();
                        ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:16:
./binary_sa_search.h:31:32: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t l = 0, r = length(sa)+1; // binary-search window
                        ˜   ˜˜˜˜˜˜˜˜˜˜^˜
./blockwise_sa.h:478:19: note: in instantiation of function template specialization 'binarySASearch<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned int>' requested here
                                        uint32_t r = binarySASearch(t, i, _sampleSuffs);
                                                     ^
./blockwise_sa.h:274:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::buildSamples' requested here
                        buildSamples();
                        ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:16:
./binary_sa_search.h:32:21: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t hostLen = length(host);
                 ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:37:
SeqAn-1.1/seqan/sequence/sequence_interface.h:1395:25: warning: implicit conversion changes signedness: 'int' to 'typename Size<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit<T>::Type());
               ˜˜˜˜˜˜˜˜˜˜˜     ^˜˜˜
SeqAn-1.1/seqan/sequence/sequence_interface.h:1444:2: note: in instantiation of function template specialization 'seqan::resizeSpace<seqan::String<unsigned int, seqan::Alloc<void> >, int, long long>' requested here
        resizeSpace(me, 0, pos, pos + 1);
        ^
./blockwise_sa.h:513:6: note: in instantiation of function template specialization 'seqan::erase<seqan::String<unsigned int, seqan::Alloc<void> >, long long>' requested here
                                        erase(_sampleSuffs, i+added);
                                        ^
./blockwise_sa.h:274:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::buildSamples' requested here
                        buildSamples();
                        ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:37:
SeqAn-1.1/seqan/sequence/sequence_interface.h:1395:9: warning: implicit conversion loses integer precision: 'typename Size<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit<T>::Type());
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:656:78: warning: implicit conversion changes signedness: 'long long' to 'typename Size<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end);
               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                             ^˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:687:52: note: in instantiation of function template specialization 'seqan::_clearSpace<unsigned int, seqan::Alloc<void>, unsigned long, long long, seqan::TagExact_>' requested here
        typename Size<String<TValue, TSpec> >::Type ret_ =_clearSpace(me, size, pos_begin, pos_end, tag);
                                                          ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1395:9: note: in instantiation of function template specialization 'seqan::resizeSpace<unsigned int, seqan::Alloc<void>, long long, seqan::TagExact_>' requested here
        return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit<T>::Type());
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1444:2: note: in instantiation of function template specialization 'seqan::resizeSpace<seqan::String<unsigned int, seqan::Alloc<void> >, int, long long>' requested here
        resizeSpace(me, 0, pos, pos + 1);
        ^
./blockwise_sa.h:513:6: note: in instantiation of function template specialization 'seqan::erase<seqan::String<unsigned int, seqan::Alloc<void> >, long long>' requested here
                                        erase(_sampleSuffs, i+added);
                                        ^
./blockwise_sa.h:274:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::buildSamples' requested here
                        buildSamples();
                        ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:656:89: warning: implicit conversion changes signedness: 'long long' to 'typename Size<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end);
               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                        ^˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:656:78: warning: implicit conversion changes signedness: 'long long' to 'typename Size<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end);
               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                             ^˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:687:52: note: in instantiation of function template specialization 'seqan::_clearSpace<unsigned int, seqan::Alloc<void>, unsigned long, long long, seqan::TagGenerous_>' requested here
        typename Size<String<TValue, TSpec> >::Type ret_ =_clearSpace(me, size, pos_begin, pos_end, tag);
                                                          ^
SeqAn-1.1/seqan/sequence/string_base.h:1149:3: note: in instantiation of function template specialization 'seqan::resizeSpace<unsigned int, seqan::Alloc<void>, long long, seqan::TagGenerous_>' requested here
                resizeSpace(me, 1, pos, pos, TExpand());
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1167:2: note: in instantiation of function template specialization 'seqan::_Insert_Value_2_String<const seqan::Tag<seqan::TagGenerous_> >::insertValue_<seqan::String<unsigned int, seqan::Alloc<void> >, long long, const unsigned int>' requested here
        _Insert_Value_2_String<Tag<TExpand> const>::insertValue_(me, pos, _value);
        ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1151:2: note: in instantiation of function template specialization 'seqan::insertValue<unsigned int, seqan::Alloc<void>, long long, unsigned int, seqan::TagGenerous_>' requested here
        insertValue(me, pos, _value, typename DefaultOverflowImplicit<T>::Type());
        ^
./blockwise_sa.h:527:6: note: in instantiation of function template specialization 'seqan::insertValue<seqan::String<unsigned int, seqan::Alloc<void> >, long long, unsigned int>' requested here
                                        insertValue(_sampleSuffs, i + (added++), bucketReps[i]);
                                        ^
./blockwise_sa.h:274:4: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                        buildSamples();
                        ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:656:89: warning: implicit conversion changes signedness: 'long long' to 'typename Size<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end);
               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                        ^˜˜˜˜˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:752:17: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t len = length(t);
                 ˜˜˜   ^˜˜˜˜˜˜˜˜
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::nextBlock' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:17:
./zbox.h:47:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                while (off+q+rCur+1 < length(s) && s[off+q+rCur+1] == s[off+betaLen+q]) q++;
                                          ˜^
./blockwise_sa.h:811:5: note: in instantiation of function template specialization 'calcZ<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
                                ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::nextBlock' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:17:
./zbox.h:47:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                while (off+q+rCur+1 < length(s) && s[off+q+rCur+1] == s[off+betaLen+q]) q++;
                                                                        ˜^
./zbox.h:47:73: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                while (off+q+rCur+1 < length(s) && s[off+q+rCur+1] == s[off+betaLen+q]) q++;
                                                                                                   ˜^
./zbox.h:48:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                z[k] = betaLen + q;
                                               ˜ ^
./zbox.h:50:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                rCur = rCur + q;
                                            ˜ ^
./zbox.h:30:14: warning: implicit conversion loses integer precision: 'unsigned long' to 'typename Value<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned int') [-Wshorten-64-to-32]
                        z[k] = ki - k;
                             ˜ ˜˜˜^˜˜
./zbox.h:48:20: warning: implicit conversion loses integer precision: 'unsigned long' to 'typename Value<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned int') [-Wshorten-64-to-32]
                                z[k] = betaLen + q;
                                     ˜ ˜˜˜˜˜˜˜˜^˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:641:17: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t len = length(t);
                 ˜˜˜   ^˜˜˜˜˜˜˜˜
./blockwise_sa.h:856:29: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::suffixCmp' requested here
                                if(hi != 0xffffffff && !suffixCmp(hi, i, jHi, kHi, kHiSoft, zHi)) {
                                                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::nextBlock' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:653:20: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t zIdx = i-j;
                         ˜˜˜˜   ˜^˜
./blockwise_sa.h:694:9: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                l = k - i; // point to just after previous match
                  ˜ ˜˜^˜˜
./blockwise_sa.h:580:18: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t tlen = length(t);
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜
./blockwise_sa.h:665:15: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::tieBreakingLcp' requested here
                        bool ret = tieBreakingLcp(i, cmp, l, kSoft);
                                   ^
./blockwise_sa.h:856:29: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::suffixCmp' requested here
                                if(hi != 0xffffffff && !suffixCmp(hi, i, jHi, kHi, kHiSoft, zHi)) {
                                                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::nextBlock' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:323:18: warning: implicit conversion loses integer precision: 'typename Size<const String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t slen = seqan::length(bucket);
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::qsort' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:324:17: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t len = seqan::length(t);
                 ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:331:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
                mkeyQSortSufDcU8(t, host, len, s, slen, *_dc,
                ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::qsort' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1079:10: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1098:30: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1108:30: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1064:65: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                       ^˜˜˜˜
./multikey_qsort.h:1064:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                              ^˜˜
./multikey_qsort.h:1073:65: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                       ^˜˜˜˜
./multikey_qsort.h:1073:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                              ^˜˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1079:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1079:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1079:32: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1098:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1098:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1098:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1108:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1108:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1108:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:748:14: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        size_t a = (rand() % n) + begin; // choose pivot between begin and end
                    ^˜˜˜˜˜ ˜
./multikey_qsort.h:1062:3: note: in instantiation of function template specialization 'qsortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
                qsortSufDcU8<T1,T2>(seqanHost, host, hlen, s, slen, dc, begin, end, sanityCheck);
                ^
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:331:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
                mkeyQSortSufDcU8(t, host, len, s, slen, *_dc,
                ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::qsort' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:977:39: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                               0xffffffff, begin, end);
                                                           ^˜˜˜˜
./multikey_qsort.h:1070:3: note: in instantiation of function template specialization 'bucketSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
                bucketSortSufDcU8(seqanHost, host, hlen, s, slen, dc,
                ^
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:331:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
                mkeyQSortSufDcU8(t, host, len, s, slen, *_dc,
                ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::qsort' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:977:46: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                               0xffffffff, begin, end);
                                                                  ^˜˜
./multikey_qsort.h:982:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t off = depth+s[i];
                         ˜˜˜   ˜˜˜˜˜^˜˜˜˜
./multikey_qsort.h:992:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t cur = begin + cnts[0];
                 ˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./multikey_qsort.h:1000:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cur = begin;
            ˜ ^˜˜˜˜
./multikey_qsort.h:852:41: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                               0xffffffff, begin, end);
                                                                           ^˜˜˜˜
./multikey_qsort.h:973:3: note: in instantiation of function template specialization 'selectionSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
                selectionSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi,
                ^
./multikey_qsort.h:1070:3: note: in instantiation of function template specialization 'bucketSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
                bucketSortSufDcU8(seqanHost, host, hlen, s, slen, dc,
                ^
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:331:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, unsigned char *>' requested here
                mkeyQSortSufDcU8(t, host, len, s, slen, *_dc,
                ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::qsort' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:852:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                               0xffffffff, begin, end);
                                                                                  ^˜˜
./multikey_qsort.h:856:20: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        v = off - depth + 1;
                          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./multikey_qsort.h:863:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t targ = i;
                         ˜˜˜˜   ^
./multikey_qsort.h:864:28: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t targoff = depth + s[i];
                         ˜˜˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:867:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        uint32_t joff = depth + s[j];
                                 ˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:883:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        targ = j;
                                             ˜ ^
./multikey_qsort.h:899:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                targ = j;
                                                     ˜ ^
./multikey_qsort.h:916:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        targ = j;
                                             ˜ ^
./multikey_qsort.h:937:38: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                       0xffffffff, begin, end);
                                                   ^˜˜˜˜
./multikey_qsort.h:937:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                       0xffffffff, begin, end);
                                                          ^˜˜
In file included from ebwt_build.cpp:11:
./ebwt.h:2968:45: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                mmFile[i] = (char*)mmap((void *)0, sbuf.st_size,
                                                   ˜˜˜˜            ˜˜˜˜˜^˜˜˜˜˜˜
./ebwt.h:511:4: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::readIntoMemory' requested here
                        readIntoMemory(
                        ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
./ebwt.h:3035:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  lineRate     = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜˜       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3037:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  linesPerSide = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3039:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  offRate      = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3045:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  ftabChars    = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3049:18: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t flags = readI32(_in1, switchEndian);
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3096:34: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                offRateDiff = _overrideOffRate - offRate;
                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./ebwt.h:3110:34: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                isaRateDiff = _overrideIsaRate - isaRate;
                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./ebwt.h:1737:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memset(seen, 0, 4 * seenLen);
        ˜˜˜˜˜˜          ˜˜^˜˜˜˜˜˜˜˜
./ebwt.h:519:4: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::sanityCheckAll' requested here
                        sanityCheckAll(refparams.reverse);
                        ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:11:
./ebwt.h:1767:25: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
        sanityCheckUpToSide(eh._numSides);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜
./ebwt.h:1675:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        while(cur < (upToSide * eh._sideSz)) {
                     ^˜˜˜˜˜˜˜ ˜
./ebwt.h:1767:2: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::sanityCheckUpToSide' requested here
        sanityCheckUpToSide(eh._numSides);
        ^
./ebwt.h:519:4: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::sanityCheckAll' requested here
                        sanityCheckAll(refparams.reverse);
                        ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:323:17: warning: implicit conversion loses integer precision: 'const int' to 'unsigned char' [-Wconversion]
        target.value = source;
                     ˜ ^˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:98:3: note: in instantiation of function template specialization 'seqan::assign<unsigned char, seqan::_Dna, int>' requested here
                assign(*this, other);
                ^
./ebwt.h:2827:33: note: in instantiation of function template specialization 'seqan::SimpleType<unsigned char, seqan::_Dna>::operator=<int>' requested here
                s[this->_eh._len - jumps - 1] = rowL(l);
                                              ^
ebwt_build.cpp:450:17: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::restore' requested here
                TStr s2; ebwt.restore(s2);
                              ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ebwt_build.cpp:466:7: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >' requested here
                        if(length(s2) < 1000) {
                           ^
ebwt_build.cpp:584:6: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                        driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
                                        ^
ebwt_build.cpp:429:18: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seed,         // pseudo-random number generator seed
                        ^˜˜˜
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
ebwt_build.cpp:458:5: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                seed);       // pseudo-random number generator seed
                                ^˜˜˜
ebwt_build.cpp:345:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                writeU32(fout3, szs.size(), bigEndian); // write # records
                                ˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜
ebwt_build.cpp:359:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                writeU32(fout3, szs.size(), bigEndian); // write # records
                                ˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜
ebwt_build.cpp:427:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sztot.first,  // total size of all unambiguous ref chars
                        ˜˜˜˜˜˜^˜˜˜˜
ebwt_build.cpp:456:11: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                sztot.first, // total size of all unambiguous ref chars
                                ˜˜˜˜˜˜^˜˜˜˜
In file included from ebwt_build.cpp:11:
./ebwt.h:702:69: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        size_t sz = DifferenceCoverSample<TStr>::simulateAllocs(s, dcv >> 1);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                          ˜˜˜˜^˜˜˜
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
./ebwt.h:723:46: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ˜˜˜          ^˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:32:
./ref_read.h:173:31: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                if (name) name->push_back(c);
                                          ˜˜˜˜            ^
./ebwt.h:4011:20: note: in instantiation of function template specialization 'fastaRefReadAppend<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                        RefRecord rec = fastaRefReadAppend(*l[i], first, ret, rpcp, &_refnames.back());
                                        ^
./ebwt.h:602:6: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::joinToDisk' requested here
                                        joinToDisk(is, szs, plens, sztot, refparams, s, out1, out2, seed);
                                        ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:32:
./ref_read.h:282:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return RefRecord(off, len, first);
               ˜˜˜˜˜˜˜˜˜ ^˜˜
./ref_read.h:282:24: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return RefRecord(off, len, first);
               ˜˜˜˜˜˜˜˜˜      ^˜˜
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:421:23: warning: implicit conversion changes signedness: 'int' to 'TPosition' (aka 'unsigned long') [-Wsign-conversion]
        return TIterator(me, pos_);
               ˜˜˜˜˜˜˜˜˜     ^˜˜˜
SeqAn-1.1/seqan/sequence/string_packed.h:442:9: note: in instantiation of function template specialization 'seqan::iter<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, int, seqan::TagRooted_>' requested here
        return iter(me, 0, tag_);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:261:9: note: in instantiation of function template specialization 'seqan::begin<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, seqan::TagRooted_>' requested here
        return begin(me, typename DefaultGetIteratorSpec<T>::Type()) ;
               ^
SeqAn-1.1/seqan/sequence/string_base.h:1108:20: note: in instantiation of function template specialization 'seqan::begin<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                valueConstruct(begin(me) + me_length, temp_copy); //??? this should be valueMoveConstruct
                                               ^
SeqAn-1.1/seqan/sequence/string_base.h:1128:2: note: in instantiation of function template specialization 'seqan::_Append_Value_2_String<const seqan::Tag<seqan::TagGenerous_> >::appendValue_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, const seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        _Append_Value_2_String<Tag<TExpand> const>::appendValue_(me, _value);
        ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1116:2: note: in instantiation of function template specialization 'seqan::appendValue<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> >, seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::TagGenerous_>' requested here
        appendValue(me, _value, typename DefaultOverflowImplicit<T>::Type());
        ^
./ref_read.h:247:5: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                                appendValue(dst, (Dna)dinuc2color[charToDna5[(int)c]][lc]);
                                ^
./ebwt.h:4011:20: note: in instantiation of function template specialization 'fastaRefReadAppend<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                        RefRecord rec = fastaRefReadAppend(*l[i], first, ret, rpcp, &_refnames.back());
                                        ^
./ebwt.h:602:6: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::joinToDisk' requested here
                                        joinToDisk(is, szs, plens, sztot, refparams, s, out1, out2, seed);
                                        ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:906:88: warning: implicit conversion changes signedness: 'long' to 'typename Position<const Iter<String<SimpleType<unsigned char, _Dna>, Packed<Alloc<void> > >, Packed<Alloc<void> > > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return (hostIterator(me) - begin(host_)) * _PackedConsts<TContainer>::VALUES_PER_WORD + _bitpos(me) / _PackedConsts<TContainer>::BITS_PER_VALUE;
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_packed.h:1191:63: note: in instantiation of function template specialization 'seqan::position<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void> >' requested here
        return Iter<TContainer, Packed<THostspec> >(container(left), position(left) + right);
                                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1108:30: note: in instantiation of function template specialization 'seqan::operator+<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void>, unsigned long>' requested here
                                valueConstruct(begin(me) + me_length, temp_copy); //??? this should be valueMoveConstruct
                                                         ^
SeqAn-1.1/seqan/sequence/string_base.h:1128:2: note: in instantiation of function template specialization 'seqan::_Append_Value_2_String<const seqan::Tag<seqan::TagGenerous_> >::appendValue_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, const seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        _Append_Value_2_String<Tag<TExpand> const>::appendValue_(me, _value);
        ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1116:2: note: in instantiation of function template specialization 'seqan::appendValue<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> >, seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::TagGenerous_>' requested here
        appendValue(me, _value, typename DefaultOverflowImplicit<T>::Type());
        ^
./ref_read.h:247:5: note: in instantiation of function template specialization 'seqan::appendValue<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
                                appendValue(dst, (Dna)dinuc2color[charToDna5[(int)c]][lc]);
                                ^
./ebwt.h:4011:20: note: in instantiation of function template specialization 'fastaRefReadAppend<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                        RefRecord rec = fastaRefReadAppend(*l[i], first, ret, rpcp, &_refnames.back());
                                        ^
./ebwt.h:602:6: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::joinToDisk' requested here
                                        joinToDisk(is, szs, plens, sztot, refparams, s, out1, out2, seed);
                                        ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:973:59: warning: implicit conversion changes signedness: 'int' to 'THostValue' (aka 'unsigned int') [-Wsign-conversion]
        THostValue mask_ = _PackedConsts<TContainer>::VALUE_MASK << _bitpos(me);
                   ˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_packed.h:999:2: note: in instantiation of function template specialization 'seqan::_assignValue_packed_string_iterator<const seqan::Iter<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Packed<seqan::Alloc<void> > >, seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        _assignValue_packed_string_iterator(me, _temp_value);
        ^
SeqAn-1.1/seqan/sequence/string_packed.h:1038:2: note: in instantiation of function template specialization 'seqan::assignValue<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void>, seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        assignValue(it, param_);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:1108:5: note: in instantiation of function template specialization 'seqan::valueConstruct<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void>, seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
                                valueConstruct(begin(me) + me_length, temp_copy); //??? this should be valueMoveConstruct
                                ^
SeqAn-1.1/seqan/sequence/string_base.h:1128:2: note: in instantiation of function template specialization 'seqan::_Append_Value_2_String<const seqan::Tag<seqan::TagGenerous_> >::appendValue_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, const seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        _Append_Value_2_String<Tag<TExpand> const>::appendValue_(me, _value);
        ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1116:2: note: in instantiation of function template specialization 'seqan::appendValue<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> >, seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::TagGenerous_>' requested here
        appendValue(me, _value, typename DefaultOverflowImplicit<T>::Type());
        ^
./ref_read.h:247:5: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                                appendValue(dst, (Dna)dinuc2color[charToDna5[(int)c]][lc]);
                                ^
./ebwt.h:4011:20: note: in instantiation of function template specialization 'fastaRefReadAppend<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                        RefRecord rec = fastaRefReadAppend(*l[i], first, ret, rpcp, &_refnames.back());
                                        ^
./ebwt.h:602:6: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::joinToDisk' requested here
                                        joinToDisk(is, szs, plens, sztot, refparams, s, out1, out2, seed);
                                        ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:421:23: warning: implicit conversion changes signedness: 'int' to 'TPosition' (aka 'unsigned long') [-Wsign-conversion]
        return TIterator(me, pos_);
               ˜˜˜˜˜˜˜˜˜     ^˜˜˜
SeqAn-1.1/seqan/sequence/string_packed.h:442:9: note: in instantiation of function template specialization 'seqan::iter<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, int, seqan::TagStandard_>' requested here
        return iter(me, 0, tag_);
               ^
SeqAn-1.1/seqan/sequence/string_base.h:1113:19: note: in instantiation of function template specialization 'seqan::begin<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, seqan::TagStandard_>' requested here
                        valueConstruct(begin(me, Standard()) + me_length, _value);
                                       ^
SeqAn-1.1/seqan/sequence/string_base.h:1128:2: note: in instantiation of function template specialization 'seqan::_Append_Value_2_String<const seqan::Tag<seqan::TagGenerous_> >::appendValue_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, const seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        _Append_Value_2_String<Tag<TExpand> const>::appendValue_(me, _value);
        ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1116:2: note: in instantiation of function template specialization 'seqan::appendValue<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> >, seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::TagGenerous_>' requested here
        appendValue(me, _value, typename DefaultOverflowImplicit<T>::Type());
        ^
./ref_read.h:247:5: note: in instantiation of function template specialization 'seqan::appendValue<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
                                appendValue(dst, (Dna)dinuc2color[charToDna5[(int)c]][lc]);
                                ^
./ebwt.h:4011:20: note: in instantiation of function template specialization 'fastaRefReadAppend<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                        RefRecord rec = fastaRefReadAppend(*l[i], first, ret, rpcp, &_refnames.back());
                                        ^
./ebwt.h:602:6: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::joinToDisk' requested here
                                        joinToDisk(is, szs, plens, sztot, refparams, s, out1, out2, seed);
                                        ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:973:59: warning: implicit conversion changes signedness: 'int' to 'THostValue' (aka 'unsigned int') [-Wsign-conversion]
        THostValue mask_ = _PackedConsts<TContainer>::VALUE_MASK << _bitpos(me);
                   ˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_packed.h:989:2: note: in instantiation of function template specialization 'seqan::_assignValue_packed_string_iterator<seqan::Iter<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Packed<seqan::Alloc<void> > >, seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        _assignValue_packed_string_iterator(me, _temp_value);
        ^
SeqAn-1.1/seqan/basic/basic_proxy.h:117:3: note: in instantiation of function template specialization 'seqan::assignValue<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void>, seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
                assignValue(data_iterator, getValue(_other.data_iterator));
                ^
./ref_read.h:277:12: note: in instantiation of member function 'seqan::Proxy<seqan::IteratorProxy<seqan::Iter<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Packed<seqan::Alloc<void> > > > >::operator=' requested here
                                dst[i] = dst[j];
                                       ^
./ebwt.h:4011:20: note: in instantiation of function template specialization 'fastaRefReadAppend<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                        RefRecord rec = fastaRefReadAppend(*l[i], first, ret, rpcp, &_refnames.back());
                                        ^
./ebwt.h:602:6: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::joinToDisk' requested here
                                        joinToDisk(is, szs, plens, sztot, refparams, s, out1, out2, seed);
                                        ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
./ebwt.h:555:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        writeU32(os, seqm1,  this->toBe()); // sequence id
                        ˜˜˜˜˜˜˜˜     ^˜˜˜˜
./ebwt.h:608:6: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::szsToDisk' requested here
                                        szsToDisk(tmp, out1, refparams.reverse);
                                        ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
./ebwt.h:556:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        writeU32(os, fwoff,  this->toBe()); // offset into sequence
                        ˜˜˜˜˜˜˜˜     ^˜˜˜˜
./ebwt.h:4193:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        int sideCur = eh._sideBwtSz - 1;
            ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:727:5: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::buildToDisk' requested here
                                buildToDisk(bsa, s, out1, out2);
                                ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
./ebwt.h:4266:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                sufInt |= (unsigned char)(Dna)(s[saElt+i]);
                                                                                      ˜^
./ebwt.h:4354:28: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        sideCur = eh._sideBwtSz - 1;
                                ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:4437:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        eftabLen = eh._ftabChars*2;
                 ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:523:6: warning: implicit conversion loses integer precision: 'typename Size<const String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                _d(length(_ds)),
                  ˜^˜˜˜˜˜˜˜˜˜˜
./blockwise_sa.h:268:14: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::DifferenceCoverSample' requested here
                        _dc = new TDC(this->text(), _dcV, this->verbose(), this->sanityCheck());
                                  ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:535:59: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'typename Value<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned int') [-Wshorten-64-to-32]
                for(size_t i = 0; i < length(_ds); i++) _dInv[_ds[i]] = i;
                                                                      ˜ ^
./diff_sample.h:783:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'typename Value<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sPrimeOrder[i] = i;
                                       ˜ ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:851:59: warning: implicit conversion loses integer precision: 'typename Size<const String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
                createSuffixArray(sPrime, _isaPrime, LarssonSadakane(), length(_isaPrime));
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./diff_sample.h:684:18: warning: implicit conversion loses integer precision: 'TSize' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t tlen = length(t);
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜
./diff_sample.h:773:2: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::buildSPrime' requested here
        buildSPrime(sPrime);
        ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:662:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'typename Value<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sorted[_isaPrime[doi]] = v*i + d;
                                               ˜ ˜˜˜˜^˜˜
./diff_sample.h:867:26: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::doBuiltSanityCheck' requested here
        if(this->sanityCheck()) doBuiltSanityCheck();
                                ^
./blockwise_sa.h:269:9: note: in instantiation of member function 'DifferenceCoverSample<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::build' requested here
                        _dc->build();
                             ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:383:17: warning: implicit conversion loses integer precision: 'TSize' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t len = length(this->text());
                 ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./blockwise_sa.h:274:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::buildSamples' requested here
                        buildSamples();
                        ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:445:45: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t numBuckets = length(_sampleSuffs)+1;
                         ˜˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:16:
./binary_sa_search.h:31:32: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t l = 0, r = length(sa)+1; // binary-search window
                        ˜   ˜˜˜˜˜˜˜˜˜˜^˜
./blockwise_sa.h:478:19: note: in instantiation of function template specialization 'binarySASearch<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, unsigned int>' requested here
                                        uint32_t r = binarySASearch(t, i, _sampleSuffs);
                                                     ^
./blockwise_sa.h:274:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::buildSamples' requested here
                        buildSamples();
                        ^
./blockwise_sa.h:248:4: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::build' requested here
                        build();
                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::reset' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:16:
./binary_sa_search.h:32:21: warning: implicit conversion loses integer precision: 'TSize' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t hostLen = length(host);
                 ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:752:17: warning: implicit conversion loses integer precision: 'TSize' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t len = length(t);
                 ˜˜˜   ^˜˜˜˜˜˜˜˜
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::nextBlock' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:17:
./zbox.h:47:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                while (off+q+rCur+1 < length(s) && s[off+q+rCur+1] == s[off+betaLen+q]) q++;
                                          ˜^
./blockwise_sa.h:811:5: note: in instantiation of function template specialization 'calcZ<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
                                ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::nextBlock' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:17:
./zbox.h:47:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                while (off+q+rCur+1 < length(s) && s[off+q+rCur+1] == s[off+betaLen+q]) q++;
                                                                        ˜^
./zbox.h:47:73: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                while (off+q+rCur+1 < length(s) && s[off+q+rCur+1] == s[off+betaLen+q]) q++;
                                                                                                   ˜^
./zbox.h:48:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                z[k] = betaLen + q;
                                               ˜ ^
./zbox.h:50:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                rCur = rCur + q;
                                            ˜ ^
./zbox.h:30:14: warning: implicit conversion loses integer precision: 'unsigned long' to 'typename Value<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned int') [-Wshorten-64-to-32]
                        z[k] = ki - k;
                             ˜ ˜˜˜^˜˜
./zbox.h:48:20: warning: implicit conversion loses integer precision: 'unsigned long' to 'typename Value<String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned int') [-Wshorten-64-to-32]
                                z[k] = betaLen + q;
                                     ˜ ˜˜˜˜˜˜˜˜^˜˜
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:641:17: warning: implicit conversion loses integer precision: 'TSize' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t len = length(t);
                 ˜˜˜   ^˜˜˜˜˜˜˜˜
./blockwise_sa.h:856:29: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::suffixCmp' requested here
                                if(hi != 0xffffffff && !suffixCmp(hi, i, jHi, kHi, kHiSoft, zHi)) {
                                                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::nextBlock' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:653:20: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t zIdx = i-j;
                         ˜˜˜˜   ˜^˜
./blockwise_sa.h:694:9: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                l = k - i; // point to just after previous match
                  ˜ ˜˜^˜˜
./blockwise_sa.h:580:18: warning: implicit conversion loses integer precision: 'TSize' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t tlen = length(t);
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜
./blockwise_sa.h:665:15: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::tieBreakingLcp' requested here
                        bool ret = tieBreakingLcp(i, cmp, l, kSoft);
                                   ^
./blockwise_sa.h:856:29: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::suffixCmp' requested here
                                if(hi != 0xffffffff && !suffixCmp(hi, i, jHi, kHi, kHiSoft, zHi)) {
                                                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::nextBlock' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:431:23: warning: implicit conversion changes signedness: 'long long' to 'TPosition' (aka 'unsigned long') [-Wsign-conversion]
        return TIterator(me, pos_);
               ˜˜˜˜˜˜˜˜˜     ^˜˜˜
SeqAn-1.1/seqan/sequence/string_packed.h:494:10: note: in instantiation of function template specialization 'seqan::iter<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, long long, seqan::TagStandard_>' requested here
        return *iter(me, pos, Standard());
                ^
SeqAn-1.1/seqan/sequence/string_packed.h:134:10: note: in instantiation of function template specialization 'seqan::value<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, long long>' requested here
                return value(*this, pos);
                       ^
./blockwise_sa.h:685:47: note: in instantiation of function template specialization 'seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >::operator[]<long long>' requested here
                while(l < len-cmp && k < len && t[cmp+l] == t[k]) {
                                                            ^
./blockwise_sa.h:856:29: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::suffixCmp' requested here
                                if(hi != 0xffffffff && !suffixCmp(hi, i, jHi, kHi, kHiSoft, zHi)) {
                                                        ^
./ebwt.h:723:33: note: in instantiation of member function 'KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::nextBlock' requested here
                                KarkkainenBlockwiseSA<TStr> bsa(s, bmax, dcv, seed, _sanity, _passMemExc, _verbose);
                                                            ^
./ebwt.h:468:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::initFromVector' requested here
                initFromVector(
                ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
./ebwt.h:2968:45: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                mmFile[i] = (char*)mmap((void *)0, sbuf.st_size,
                                                   ˜˜˜˜            ˜˜˜˜˜^˜˜˜˜˜˜
./ebwt.h:511:4: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::readIntoMemory' requested here
                        readIntoMemory(
                        ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
./ebwt.h:3035:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  lineRate     = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜˜       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3037:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  linesPerSide = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3039:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  offRate      = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3045:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  ftabChars    = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3049:18: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t flags = readI32(_in1, switchEndian);
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3096:34: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                offRateDiff = _overrideOffRate - offRate;
                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./ebwt.h:3110:34: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                isaRateDiff = _overrideIsaRate - isaRate;
                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./ebwt.h:1737:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memset(seen, 0, 4 * seenLen);
        ˜˜˜˜˜˜          ˜˜^˜˜˜˜˜˜˜˜
./ebwt.h:519:4: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::sanityCheckAll' requested here
                        sanityCheckAll(refparams.reverse);
                        ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
./ebwt.h:1767:25: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
        sanityCheckUpToSide(eh._numSides);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜
./ebwt.h:1675:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        while(cur < (upToSide * eh._sideSz)) {
                     ^˜˜˜˜˜˜˜ ˜
./ebwt.h:1767:2: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::sanityCheckUpToSide' requested here
        sanityCheckUpToSide(eh._numSides);
        ^
./ebwt.h:519:4: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::sanityCheckAll' requested here
                        sanityCheckAll(refparams.reverse);
                        ^
ebwt_build.cpp:411:13: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::Ebwt' requested here
        Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
                   ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
./ebwt.h:2035:69: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
        if(c == 0 && l._sideByteOff <= _zEbwtByteOff && l._sideByteOff + l._by >= _zEbwtByteOff) {
                                                                       ˜ ˜˜^˜˜
./ebwt.h:2311:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::countFwSide' requested here
        if(l._fw) ret = countFwSide(l, c); // Forward side
                        ^
./ebwt.h:2825:19: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::mapLF' requested here
                uint32_t newi = mapLF(l);
                                ^
ebwt_build.cpp:450:17: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::restore' requested here
                TStr s2; ebwt.restore(s2);
                              ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
./ebwt.h:2038:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                if((l._sideByteOff + l._by > _zEbwtByteOff) ||
                                   ˜ ˜˜^˜˜
./ebwt.h:2039:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                   (l._sideByteOff + l._by == _zEbwtByteOff && l._bp > _zEbwtBpOff))
                                   ˜ ˜˜^˜˜
./ebwt.h:1945:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                cCnt += countInU64(c, *(uint64_t*)&side[i]);
                     ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:2033:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::countUpTo' requested here
        uint32_t cCnt = countUpTo(l, c);
                        ^
./ebwt.h:2311:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::countFwSide' requested here
        if(l._fw) ret = countFwSide(l, c); // Forward side
                        ^
./ebwt.h:2825:19: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::mapLF' requested here
                uint32_t newi = mapLF(l);
                                ^
ebwt_build.cpp:450:17: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::restore' requested here
                TStr s2; ebwt.restore(s2);
                              ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
./ebwt.h:2140:69: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
        if(c == 0 && l._sideByteOff <= _zEbwtByteOff && l._sideByteOff + l._by >= _zEbwtByteOff) {
                                                                       ˜ ˜˜^˜˜
./ebwt.h:2312:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::countBwSide' requested here
        else      ret = countBwSide(l, c); // Backward side
                        ^
./ebwt.h:2825:19: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::mapLF' requested here
                uint32_t newi = mapLF(l);
                                ^
ebwt_build.cpp:450:17: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >::restore' requested here
                TStr s2; ebwt.restore(s2);
                              ^
ebwt_build.cpp:595:5: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                                driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
                                ^
In file included from ebwt_build.cpp:11:
./ebwt.h:2143:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                if((l._sideByteOff + l._by > _zEbwtByteOff) ||
                                   ˜ ˜˜^˜˜
./ebwt.h:2144:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                   (l._sideByteOff + l._by == _zEbwtByteOff && l._bp >= _zEbwtBpOff))
                                   ˜ ˜˜^˜˜
713 warnings generated.
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:52:
SeqAn-1.1/seqan/basic/basic_profile.h:161:14: warning: implicit conversion changes signedness: '_proInt' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
        return (_proData<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:54:
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:70:22: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
        const int DEFAULT = ˜(˜0u >> 1); // initialize with the smallest int
                  ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:229:116: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
                finline static void run(unsigned char* ptr, unsigned char c) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
                                                                                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1131:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1140:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char)c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1149:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1167:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1178:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna5<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1187:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1196:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1205:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna5<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1226:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Iupac<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1235:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1244:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1251:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1258:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1269:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_AA<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1278:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1287:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:46:
SeqAn-1.1/seqan/file/cstream.h:142:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return getc(source);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:170:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:181:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:193:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
SeqAn-1.1/seqan/file/cstream.h:205:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:12:
In file included from ./alphabet.h:9:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:14:
./filebuf.h:73:61: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(_lastn_cur < LASTN_BUF_SZ) _lastn_buf[_lastn_cur++] = c;
                                                                               ˜ ^
./filebuf.h:158:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _inf->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:161:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _ins->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:478:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = slen;
                                     ˜ ^˜˜˜
./filebuf.h:505:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = len;
                                     ˜ ^˜˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:15:
In file included from ./word_io.h:8:
./endian_swap.h:23:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        tmp |= ((u << 24) & (0xff << 24));
                          ˜  ˜˜˜˜˜^˜˜˜˜
./endian_swap.h:32:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 56) & (0xffull <<  0));
                             ^
./endian_swap.h:33:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 40) & (0xffull <<  8));
                             ^
./endian_swap.h:34:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 24) & (0xffull << 16));
                             ^
./endian_swap.h:35:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >>  8) & (0xffull << 24));
                             ^
./endian_swap.h:36:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u <<  8) & (0xffull << 32));
                             ^
./endian_swap.h:37:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 24) & (0xffull << 40));
                             ^
./endian_swap.h:38:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 40) & (0xffull << 48));
                             ^
./endian_swap.h:39:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 56) & (0xffull << 56));
                             ^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:15:
./word_io.h:119:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return endianSwapI32(x);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./word_io.h:121:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return x;
                ˜˜˜˜˜˜ ^
./word_io.h:135:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return endianSwapI32(x);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./word_io.h:137:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return x;
                ˜˜˜˜˜˜ ^
In file included from ref_read.cpp:1:
./ref_read.h:173:31: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                if (name) name->push_back(c);
                                          ˜˜˜˜            ^
ref_read.cpp:61:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, len, first);
                               ˜˜˜˜˜˜˜˜˜ ^˜˜
ref_read.cpp:61:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, len, first);
                               ˜˜˜˜˜˜˜˜˜      ^˜˜
ref_read.cpp:98:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, 0, first);
                               ˜˜˜˜˜˜˜˜˜ ^˜˜
ref_read.cpp:109:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, 0, first);
                               ˜˜˜˜˜˜˜˜˜ ^˜˜
ref_read.cpp:148:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, len, first);
                               ˜˜˜˜˜˜˜˜˜ ^˜˜
ref_read.cpp:148:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, len, first);
                               ˜˜˜˜˜˜˜˜˜      ^˜˜
ref_read.cpp:165:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return RefRecord(off, len, first);
               ˜˜˜˜˜˜˜˜˜ ^˜˜
ref_read.cpp:165:24: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return RefRecord(off, len, first);
               ˜˜˜˜˜˜˜˜˜      ^˜˜
ref_read.cpp:188:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        bool first = (i == (int)src.size()-1 || src[i+1].first);
                                                                ˜˜˜ ˜^˜
ref_read.cpp:189:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if(src[i].len) {
                           ˜˜˜ ^
ref_read.cpp:190:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                cur.push_back(RefRecord(0, src[i].len, first));
                                                           ˜˜˜ ^
ref_read.cpp:193:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if(src[i].off) cur.push_back(RefRecord(src[i].off, 0, first));
                           ˜˜˜ ^
ref_read.cpp:193:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if(src[i].off) cur.push_back(RefRecord(src[i].off, 0, first));
                                                               ˜˜˜ ^
ref_read.cpp:197:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if(i < (int)cur.size()-1 && cur[i].off != 0 && !cur[i+1].first) {
                                                    ˜˜˜ ^
ref_read.cpp:197:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if(i < (int)cur.size()-1 && cur[i].off != 0 && !cur[i+1].first) {
                                                                        ˜˜˜ ˜^˜
ref_read.cpp:198:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                dst.push_back(RefRecord(cur[i].off, cur[i+1].len, cur[i].first));
                                                        ˜˜˜ ^
ref_read.cpp:198:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                dst.push_back(RefRecord(cur[i].off, cur[i+1].len, cur[i].first));
                                                                    ˜˜˜ ˜^˜
ref_read.cpp:198:59: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                dst.push_back(RefRecord(cur[i].off, cur[i+1].len, cur[i].first));
                                                                                  ˜˜˜ ^
ref_read.cpp:201:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                dst.push_back(cur[i]);
                                              ˜˜˜ ^
ref_read.cpp:187:25: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                for(int i = src.size()-1; i >= 0; i--) {
                        ˜   ˜˜˜˜˜˜˜˜˜˜^˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:77:16: note: in instantiation of function template specialization 'seqan::length<char, seqan::Alloc<void> >' requested here
        size_t plen = length(path);
                      ^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./alphabet.h:144:19: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >' requested here
        size_t readLen = seqan::length(read);
                         ^
66 warnings generated.
In file included from edit.cpp:9:
In file included from ./edit.h:13:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from edit.cpp:9:
In file included from ./edit.h:14:
./filebuf.h:73:61: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(_lastn_cur < LASTN_BUF_SZ) _lastn_buf[_lastn_cur++] = c;
                                                                               ˜ ^
./filebuf.h:158:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _inf->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:161:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _ins->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:478:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = slen;
                                     ˜ ^˜˜˜
./filebuf.h:505:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = len;
                                     ˜ ^˜˜
In file included from edit.cpp:9:
./edit.h:36:7: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                   ˜^˜
./edit.h:36:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                      ˜^˜
./edit.h:36:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                               ˜^˜
9 warnings generated.
In file included from tinythread.cpp:25:
./tinythread.h:631:9: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
typedef long long __intmax_t;
        ^
tinythread.cpp:279:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  return (int) sysconf(_SC_NPROCESSORS_ONLN);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
bowtie_build_main.cpp:46:27: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        lastret = bowtie_build(args.size(), myargs);
                                  ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -O3  -DCOMPILER_OPTIONS="\"-O3   -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion\""  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion \
		-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
		-I SeqAn-1.1 \
		-o bowtie ebwt_search.cpp \
		ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
		-lpthread 
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:52:
SeqAn-1.1/seqan/basic/basic_profile.h:161:14: warning: implicit conversion changes signedness: '_proInt' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
        return (_proData<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:54:
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:70:22: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
        const int DEFAULT = ˜(˜0u >> 1); // initialize with the smallest int
                  ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:229:116: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
                finline static void run(unsigned char* ptr, unsigned char c) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
                                                                                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1131:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1140:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char)c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1149:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1167:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1178:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna5<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1187:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1196:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1205:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna5<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1226:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Iupac<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1235:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1244:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1251:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1258:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1269:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_AA<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1278:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1287:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search.cpp:11:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:46:
SeqAn-1.1/seqan/file/cstream.h:142:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return getc(source);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:170:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:181:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:193:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
SeqAn-1.1/seqan/file/cstream.h:205:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
In file included from ebwt_search.cpp:11:
In file included from ./alphabet.h:9:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from ebwt_search.cpp:13:
./endian_swap.h:23:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        tmp |= ((u << 24) & (0xff << 24));
                          ˜  ˜˜˜˜˜^˜˜˜˜
./endian_swap.h:32:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 56) & (0xffull <<  0));
                             ^
./endian_swap.h:33:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 40) & (0xffull <<  8));
                             ^
./endian_swap.h:34:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 24) & (0xffull << 16));
                             ^
./endian_swap.h:35:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >>  8) & (0xffull << 24));
                             ^
./endian_swap.h:36:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u <<  8) & (0xffull << 32));
                             ^
./endian_swap.h:37:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 24) & (0xffull << 40));
                             ^
./endian_swap.h:38:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 40) & (0xffull << 48));
                             ^
./endian_swap.h:39:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 56) & (0xffull << 56));
                             ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:16:
In file included from SeqAn-1.1/seqan/index.h:83:
SeqAn-1.1/seqan/index/shape_gapped.h:583:12: warning: implicit conversion changes signedness: 'unsigned int' to 'typename Value<String<int, Alloc<void> > >::Type' (aka 'int') [-Wsign-conversion]
                                *itS = diff;
                                     ˜ ^˜˜˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:26:
./bitpack.h:26:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        thirty2 |= (two << (off*2));
                ˜˜  ˜˜˜˜^˜˜˜˜˜˜˜˜˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
In file included from ./pat.h:17:
In file included from ./threading.h:5:
./tinythread.h:631:9: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
typedef long long __intmax_t;
        ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
In file included from ./pat.h:18:
./filebuf.h:73:61: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(_lastn_cur < LASTN_BUF_SZ) _lastn_buf[_lastn_cur++] = c;
                                                                               ˜ ^
./filebuf.h:158:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _inf->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:161:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _ins->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:478:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = slen;
                                     ˜ ^˜˜˜
./filebuf.h:505:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = len;
                                     ˜ ^˜˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
In file included from ./pat.h:19:
./qual.h:93:40: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
                char cc = solexaToPhred((int)c - 64) + 33;
                     ˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./qual.h:147:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return (int)pQ;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜
./qual.h:161:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:165:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./qual.h:188:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:191:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
In file included from ./pat.h:20:
In file included from ./hit_set.h:16:
./edit.h:36:7: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                   ˜^˜
./edit.h:36:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                      ˜^˜
./edit.h:36:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                               ˜^˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
In file included from ./pat.h:20:
./hit_set.h:37:12: warning: implicit conversion changes signedness: 'const uint8_t' (aka 'const unsigned char') to 'char' [-Wsign-conversion]
                fb.write(fw);
                ˜˜       ^˜
./hit_set.h:44:17: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t sz = edits.size();
                         ˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:50:8: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                sz = cedits.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:63:8: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                fw = fb.get();
                   ˜ ^˜˜˜˜˜˜˜
./hit_set.h:65:13: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                stratum = fb.get();
                        ˜ ^˜˜˜˜˜˜˜
./hit_set.h:244:16: warning: implicit conversion loses integer precision: 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t i = seqan::length(name);
                         ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:248:7: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = seqan::length(seq);
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:256:7: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = ents.size();
                  ˜ ^˜˜˜˜˜˜˜˜˜˜
./hit_set.h:298:18: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                maxedStratum = fb.get();
                             ˜ ^˜˜˜˜˜˜˜
./hit_set.h:391:29: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                ents.erase(ents.begin() + i);
                           ˜˜˜˜           ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
In file included from ./sequence_io.h:12:
./pat.h:53:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:61:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:70:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:167:10: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                return seqan::length(patFw);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:723:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t ret = 0llu;
                               ^
./pat.h:728:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                return make_pair(ret, 0llu);
                                      ^
./pat.h:875:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                ^
./pat.h:875:32: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                             ^
./pat.h:1087:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1105:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1126:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, length);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1128:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, length);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:1129:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                itoa10(patid, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜
./pat.h:1164:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1169:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1183:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                patid_ += numthreads_;
                       ˜˜ ^˜˜˜˜˜˜˜˜˜˜
./pat.h:1188:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1189:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1358:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        s.erase(0, mytrim5);
                                        ˜          ^˜˜˜˜˜˜
./pat.h:1362:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        s.erase(s.length()-trim3_);
                                                          ˜^˜˜˜˜˜
./pat.h:1374:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        vq.erase(0, mytrim5);
                                        ˜˜          ^˜˜˜˜˜˜
./pat.h:1378:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        vq.erase(vq.length()-trim3_);
                                                            ˜^˜˜˜˜˜
./pat.h:1425:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1467:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1824:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:1829:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1847:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:1848:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:1871:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1892:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1898:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1887:21: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                patid = readCnt_-1;
                                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:1895:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:1897:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:1902:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2031:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2081:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2124:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2161:44: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(r2 != NULL) (*r2).nameBuf[nameLen] = c;
                                                              ˜ ^
./pat.h:2162:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:2165:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2168:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength((*r2).name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2175:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2179:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength((*r2).name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2172:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2174:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2177:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, (*r2).nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2208:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2209:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2240:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2264:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2276:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                c2 = c;
                                   ˜ ^
./pat.h:2284:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2286:25: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                c = charToPhred33(c, solQuals_, phred64Quals_);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2288:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.qualBuf[off] = c;
                                                               ˜ ^
./pat.h:2300:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2303:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        c2 = c;
                           ˜ ^
./pat.h:2332:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                nameChars_(0), bufCur_(0), subReadCnt_(0llu)
                                                       ^
./pat.h:2361:32: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                nameBuf_[nameChars_++] = c;
                                                                       ˜ ^
./pat.h:2379:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        buf_[bufCur_++] = c;
                                                        ˜ ^
./pat.h:2408:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
                                        itoa10(readCnt_ - subReadCnt_, &r.nameBuf[nameChars_]);
                                        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2414:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        patid = readCnt_-1;
                                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2574:28: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                r.nameBuf[nameLen++] = c;
                                                     ˜ ^
./pat.h:2578:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _setLength(r.name, nameLen);
                                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2586:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2608:18: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.primer = c;
                                                         ˜ ^
./pat.h:2609:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.trimc = c2;
                                                        ˜ ^˜
./pat.h:2664:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.patFw, dstLen);
                        ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:2683:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = qualsRead - mytrim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2702:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2731:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = (*qualsReadCur) - trim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2733:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        c = charToPhred33(c, solQuals_, phred64Quals_);
                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2735:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        qbuf[off] = c;
                                                                  ˜ ^
./pat.h:2755:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2792:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altPatFw[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜
./pat.h:2794:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altQual[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜
./pat.h:2816:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2813:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, r.nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2815:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                nameLen = strlen(r.nameBuf);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2822:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2929:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2930:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2944:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                size_t len = dstLen - mytrim5;
                                       ˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2959:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2961:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2973:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2970:10: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                itoa10(readCnt_, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2972:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                nameLen = strlen(r.nameBuf);
                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2976:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:3062:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
./sequence_io.h:115:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        int64_t i = 0xffffffffll;
                    ^
./sequence_io.h:138:26: warning: implicit conversion changes signedness: 'int64_t' (aka 'long long') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        stmp = stmp.substr(0, baseCutoff);
                               ˜˜˜˜           ^˜˜˜˜˜˜˜˜˜
./sequence_io.h:170:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        int64_t i = 0xffffffffll;
                    ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:651:14: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        size_t a = (rand() % n) + begin; // choose pivot between begin and end
                    ^˜˜˜˜˜ ˜
./multikey_qsort.h:748:14: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        size_t a = (rand() % n) + begin; // choose pivot between begin and end
                    ^˜˜˜˜˜ ˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:9:
./timer.h:34:40: warning: implicit conversion loses integer precision: 'long' to 'unsigned int' [-Wshorten-64-to-32]
                unsigned int hours   = (passed / 60) / 60;
                             ˜˜˜˜˜     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:16:21: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define VMSG_NL(args...) \
                    ^
./diff_sample.h:25:18: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define VMSG(args...) \
                 ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:17:
./zbox.h:48:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                z[k] = betaLen + q;
                                               ˜ ^
./zbox.h:50:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                rCur = rCur + q;
                                            ˜ ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:29:
./word_io.h:119:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return endianSwapI32(x);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./word_io.h:121:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return x;
                ˜˜˜˜˜˜ ^
./word_io.h:135:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return endianSwapI32(x);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./word_io.h:137:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return x;
                ˜˜˜˜˜˜ ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:31:
In file included from ./hit.h:15:
./bitset.h:23:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                sz &= ˜31;            // Make sure it's 32-aligned
                   ˜˜ ^˜˜
./bitset.h:511:17: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        oss << (test(i)? "1" : "0");
                                ˜˜˜˜ ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:31:
./hit.h:181:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                memset(ents_, 0, len_ << 2);
                                ˜˜˜˜˜˜           ˜˜˜˜˜^˜˜˜
./hit.h:204:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                ii = h.length() - ii - 1;
                                                ˜ ^˜
./hit.h:208:18: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        if(h.mms.test(i)) {
                           ˜          ^
./hit.h:209:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                rc = charToDna5[(int)h.refcs[i]];
                                                     ˜       ^
./hit.h:204:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                                ii = h.length() - ii - 1;
                                   ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./hit.h:316:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numAligned_(0llu),
                            ^
./hit.h:317:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numUnaligned_(0llu),
                              ^
./hit.h:318:13: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numMaxed_(0llu),
                          ^
./hit.h:319:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numReported_(0llu),
                             ^
./hit.h:320:22: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numReportedPaired_(0llu),
                                   ^
./hit.h:421:22: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                        sort(hs.begin() + start, hs.begin() + end);
                             ˜˜           ^˜˜˜˜
./hit.h:421:42: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                        sort(hs.begin() + start, hs.begin() + end);
                                                 ˜˜           ^˜˜
./hit.h:438:35: warning: implicit conversion changes signedness: 'streamoff' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        out(h.h.first).writeChars(buf, ss.tellp());
                        ˜˜˜                            ^˜˜˜˜˜˜˜˜˜
./hit.h:623:51: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:625:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:647:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:648:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:650:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:651:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:677:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:679:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:699:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:700:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:702:58: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:703:58: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:730:52: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:732:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:752:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:753:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:755:57: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:756:57: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:971:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                _numValidHits(0llu),
                              ^
./hit.h:1021:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        ret = _bufferedHits.size();
                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:1336:40: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        _bufferedHits[i].oms = (sz / mult_) - 1;
                                             ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./hit.h:1519:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                ss << "<" << h.h.first << "," << (h.h.second + offBase) << "," << h.mms.count();
                                                             ˜ ^˜˜˜˜˜˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:32:
./ref_read.h:173:31: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                if (name) name->push_back(c);
                                          ˜˜˜˜            ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:40:
./reference.h:84:41: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        mmFile = (char*)mmap((void *)0, sbuf.st_size,
                                        ˜˜˜˜            ˜˜˜˜˜^˜˜˜˜˜˜
./reference.h:313:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 0) & 3) << 24;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./reference.h:314:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 2) & 3) << 16;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./reference.h:315:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 4) & 3) << 8;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./reference.h:316:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 6) & 3) << 0;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./reference.h:318:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 0) & 3) << 0;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./reference.h:319:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 2) & 3) << 8;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./reference.h:320:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 4) & 3) << 16;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./reference.h:321:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                word |= ((i >> 6) & 3) << 24;
                                     ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./reference.h:225:25: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const value_type' (aka 'const unsigned int') [-Wshorten-64-to-32]
                refRecOffs_.push_back(recs_.size());
                ˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜˜
./reference.h:579:17: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
                                                        count -= chars;
                                                              ˜˜ ^˜˜˜˜
./reference.h:580:18: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
                                                        bufOff += chars;
                                                               ˜˜ ^˜˜˜˜
./reference.h:581:16: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
                                                        toff += chars;
                                                             ˜˜ ^˜˜˜˜
In file included from ebwt_search.cpp:14:
./ebwt.h:126:25: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                _eftabLen = _ftabChars*2;
                          ˜ ˜˜˜˜˜˜˜˜˜˜^˜
./ebwt.h:135:23: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
                _sideSz = _lineSz * _linesPerSide;
                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:140:27: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
                _numLines = _numSides * _linesPerSide;
                                      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1285:17: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                hit.stratum = stratum;
                            ˜ ^˜˜˜˜˜˜
./ebwt.h:1307:24: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.crefcs[off] = refcs[i];
                                                        ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1310:22: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.crefcs[i] = refcs[i];
                                                      ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1331:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        read[i] = (int)hit.patSeq[i];
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1332:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                        qual[i] = mmPenalty(maqRound, phredCharToPhredQual(hit.quals[i]));
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1340:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                rf[i] = (1 << rf[i]);
                                      ˜  ˜˜^˜˜˜˜˜˜˜
./ebwt.h:1356:39: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        size_t nqlen = qlen + (colExEnds ? -1 : 1);
                                            ˜              ^˜
./ebwt.h:1427:23: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.refcs[off] = refcs[i];
                                                       ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1430:29: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.refcs[mmui32[i]] = refcs[i];
                                                             ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1538:34: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        lbot._charOff = ltop._charOff + spread;
                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./ebwt.h:1544:50: warning: implicit conversion loses integer precision: 'unsigned int' to 'int16_t' (aka 'short') [-Wconversion]
                        if(!lbot._fw) lbot._by = sideBwtSz - lbot._by - 1;
                                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:1544:46: warning: implicit conversion changes signedness: 'int16_t' (aka 'short') to 'unsigned int' [-Wsign-conversion]
                        if(!lbot._fw) lbot._by = sideBwtSz - lbot._by - 1;
                                                           ˜ ˜˜˜˜˜^˜˜
./ebwt.h:1576:30: warning: implicit conversion loses integer precision: 'unsigned int' to 'int16_t' (aka 'short') [-Wconversion]
                        _by = ep._sideBwtSz - _by - 1;
                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:1576:26: warning: implicit conversion changes signedness: 'int16_t' (aka 'short') to 'unsigned int' [-Wsign-conversion]
                        _by = ep._sideBwtSz - _by - 1;
                                            ˜ ^˜˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:1607:
In file included from ./ebwt_search_backtrack.h:8:
./ebwt_search_util.h:202:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        al.u64.u64 = 0xffffffffffffffffllu;
                                     ^
./ebwt_search_util.h:266:26: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        uint32_t off = al.off.off;
                                 ˜˜˜   ˜˜˜˜˜˜˜^˜˜
./ebwt_search_util.h:324:26: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                uint16_t tpos0 = plen-1-pos0;
                         ˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜
./ebwt_search_util.h:330:51: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                appendValue(muts, QueryMutation(tpos0, oldChar, chr0)); // apply mutation
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜
./ebwt_search_util.h:335:27: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        uint16_t tpos1 = plen-1-pos1;
                                 ˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜
./ebwt_search_util.h:342:52: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                        appendValue(muts, QueryMutation(tpos1, oldChar, chr1)); // apply mutation
                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜
./ebwt_search_util.h:347:28: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                uint16_t tpos2 = plen-1-pos2;
                                         ˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜
./ebwt_search_util.h:355:48: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                                append(muts, QueryMutation(tpos2, oldChar, chr2)); // apply mutation
                                             ˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜
./ebwt_search_util.h:317:19: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t plen = length(seq);
                         ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:1607:
In file included from ./ebwt_search_backtrack.h:10:
./range_source.h:56:56: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        yetMoreEdits_ = pool.alloc(qlen + 10 - numMoreEdits - numEdits);
                                        ˜˜˜˜       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
./range_source.h:138:55: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        epool.free(yetMoreEdits_, qlen + 10 - numMoreEdits - numEdits);
                        ˜˜˜˜˜                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
./range_source.h:326:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                ret.pos = pos;
                        ˜ ^˜˜
./range_source.h:496:23: warning: operand of ? changes signedness: 'const char' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                ret.chr = color ? "0123"[chr] : "ACGT"[chr];
                                        ˜         ^˜˜˜˜˜˜˜˜˜˜
./range_source.h:496:37: warning: operand of ? changes signedness: 'const char' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                ret.chr = color ? "0123"[chr] : "ACGT"[chr];
                                        ˜                       ^˜˜˜˜˜˜˜˜˜˜
./range_source.h:515:22: warning: operand of ? changes signedness: 'const char' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        ret.chr = color ? "0123"[chr] : "ACGT"[chr];
                                ˜         ^˜˜˜˜˜˜˜˜˜˜
./range_source.h:515:36: warning: operand of ? changes signedness: 'const char' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        ret.chr = color ? "0123"[chr] : "ACGT"[chr];
                                ˜                       ^˜˜˜˜˜˜˜˜˜˜
./range_source.h:611:21: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        rangesSz_ = qlen - rdepth_;
                                  ˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜
./range_source.h:766:23: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        r = rand.nextU32() % numTiedPositions;
                          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./range_source.h:766:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        r = rand.nextU32() % numTiedPositions;
                                           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./range_source.h:779:38: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                uint16_t newRdepth = rdepth_ + pos + 1;
                         ˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./range_source.h:782:24: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                uint16_t depth = pos + rdepth_;
                         ˜˜˜˜˜   ˜˜˜˜^˜˜˜˜˜˜˜˜
./range_source.h:795:31: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                newRdepth, 0, cost_, ham_ + hamadd,
                                                     ˜˜˜˜˜^˜˜˜˜˜˜˜
./range_source.h:1636:43: warning: extra ';' inside a class [-Wextra-semi]
        ASSERT_ONLY(std::set<Branch*> branchSet_);
                                                 ^
./range_source.h:1699:54: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                foundRange(false), done(_done), minCostAdjustment_(minCostAdjustment)
                                                                  ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./range_source.h:1968:41: warning: extra ';' inside a class [-Wextra-semi]
        ASSERT_ONLY(std::set<int64_t> allTops_);
                                               ^
./range_source.h:2552:43: warning: extra ';' inside a class [-Wextra-semi]
        ASSERT_ONLY(std::set<int64_t> allTopsRc_);
                                                 ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:1607:
./ebwt_search_backtrack.h:1208:37: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        uint64_t prehits = 0xffffffffffffffffllu)
                                           ^
./ebwt_search_backtrack.h:74:11: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                _maxBts(maxBts),
                       ˜^˜˜˜˜˜
./ebwt_search_backtrack.h:79:10: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                _ihits(0llu)
                       ^
./ebwt_search_backtrack.h:223:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const unsigned int' [-Wshorten-64-to-32]
                _qlen = min<uint32_t>(length(*_qry), qlen);
                        ˜˜˜           ^˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:274:41: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        ret = reportAlignment(0, top, bot, ham);
                                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜              ^˜˜
./ebwt_search_backtrack.h:278:21: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                ret = backtrack(ftabChars, // depth
                                      ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:257:41: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const unsigned int' [-Wshorten-64-to-32]
                uint32_t m = min<uint32_t>(_unrevOff, _qlen);
                             ˜˜˜                      ^˜˜˜˜
./ebwt_search_backtrack.h:545:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        top = pairTop(pairs, d, c); bot = pairBot(pairs, d, c);
                                              ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:545:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        top = pairTop(pairs, d, c); bot = pairBot(pairs, d, c);
                                                                          ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:555:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        top = pairTop(pairs, d, c); bot = pairBot(pairs, d, c);
                                              ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:555:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        top = pairTop(pairs, d, c); bot = pairBot(pairs, d, c);
                                                                          ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:588:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        uint32_t spread = pairSpread(pairs, d, i);
                                                          ˜˜˜˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:612:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                eltop = pairTop(pairs, d, i);
                                                                        ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:613:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                elbot = pairBot(pairs, d, i);
                                                                        ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:734:54: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                bool ret = reportAlignment(stackDepth, top, bot, ham);
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                       ^˜˜
./ebwt_search_backtrack.h:833:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        j = btcint = elcint;
                                          ˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:898:23: warning: implicit conversion changes signedness: 'char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                        _refcs.push_back(btchar);
                                        ˜˜˜˜˜˜           ^˜˜˜˜˜
./ebwt_search_backtrack.h:900:27: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
                                        _refcs[stackDepth] = btchar;
                                                           ˜ ^˜˜˜˜˜
./ebwt_search_backtrack.h:911:56: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        ret = reportAlignment(stackDepth+1, bttop, btbot, btham);
                                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                             ^˜˜˜˜
./ebwt_search_backtrack.h:922:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        uint32_t ftabOff = (*_qry)[_qlen - ftabChars];
                                                                         ˜ ^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:927:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                                if(_qlen-j == icur) {
                                                        ˜^
./ebwt_search_backtrack.h:928:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                        ftabOff |= btcint;
                                                                ˜˜ ^˜˜˜˜˜
./ebwt_search_backtrack.h:931:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                                        ftabOff |= (uint32_t)(*_qry)[_qlen-j];
                                                                                          ˜^
./ebwt_search_backtrack.h:945:32: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                                ebwt._eh._ftabChars,
                                                                ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1031:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                                uint32_t spread = pairSpread(pairs, k, l);
                                                                                                  ˜˜˜˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:1046:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                                        eltop = pairTop(pairs, k, l);
                                                                                                ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:1047:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                                        elbot = pairBot(pairs, k, l);
                                                                                                ˜˜˜˜˜˜˜           ^
./ebwt_search_backtrack.h:1092:48: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        ret = reportAlignment(stackDepth, top, bot, ham);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                       ^˜˜
./ebwt_search_backtrack.h:459:28: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t cur = _qlen - d - 1; // current offset into _qry
                         ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:699:36: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                uint32_t d = _qlen - _mms[i] - 1;
                                                         ˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:776:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                icur = _qlen - i - 1; // current offset into _qry
                                                     ˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:805:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                                                btcint = j;
                                                                                       ˜ ^
./ebwt_search_backtrack.h:844:22: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                icur = _qlen - i - 1; // current offset into _qry
                                     ˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:964:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                        i+1,         // start from next position after
                                                        ˜^˜
./ebwt_search_backtrack.h:1014:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                uint32_t kcur = _qlen - k - 1; // current offset into _qry
                                                         ˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1045:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                                                        eli = k;
                                                                                            ˜ ^
./ebwt_search_backtrack.h:1144:37: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                uint32_t depth = _qlen - mms[i] - 1;
                                         ˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1189:18: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                        elims[d] = (1 << c);
                                 ˜  ˜˜^˜˜˜
./ebwt_search_backtrack.h:1252:34: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        uint32_t d = _qlen - mms[i] - 1;
                                                 ˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1355:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                uint32_t ftabOff = (*_qry)[_qlen - ftabChars];
                                                 ˜ ^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1361:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        ftabOff |= (uint32_t)(*_qry)[_qlen-i];
                                                          ˜^
./ebwt_search_backtrack.h:1417:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        if(_mms.size() <= stackDepth + i) {
                                          ^˜˜˜˜˜˜˜˜˜ ˜
./ebwt_search_backtrack.h:1421:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                _mms[stackDepth + i] = (*_muts)[i].pos;
                                     ^˜˜˜˜˜˜˜˜˜ ˜
./ebwt_search_backtrack.h:1423:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        if(_refcs.size() <= stackDepth + i) {
                                            ^˜˜˜˜˜˜˜˜˜ ˜
./ebwt_search_backtrack.h:1425:22: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                _refcs.push_back("ACGT"[(*_muts)[i].newBase]);
                                ˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1427:12: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                _refcs[stackDepth + i] = "ACGT"[(*_muts)[i].newBase];
                                       ^˜˜˜˜˜˜˜˜˜ ˜
./ebwt_search_backtrack.h:1427:30: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
                                _refcs[stackDepth + i] = "ACGT"[(*_muts)[i].newBase];
                                                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1499:28: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        promotePartialMutations(stackDepth);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1506:41: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        hit = reportFullAlignment(stackDepth + numMuts, top, bot, stratum, cost);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1554:29: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                 _qlen, stratum, cost, _patid, _seed,
                                                 ^˜˜˜˜
./ebwt_search_backtrack.h:1591:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                al.u64.u64 = 0xffffffffffffffffllu;
                             ^
./ebwt_search_backtrack.h:1608:20: warning: implicit conversion changes signedness: 'int' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
                al.entry.char0 = c;
                               ˜ ^
./ebwt_search_backtrack.h:1624:21: warning: implicit conversion changes signedness: 'int' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
                        al.entry.char1 = c;
                                       ˜ ^
./ebwt_search_backtrack.h:1639:22: warning: implicit conversion changes signedness: 'int' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
                                al.entry.char2 = c;
                                               ˜ ^
./ebwt_search_backtrack.h:1602:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t ci = _qlen - _mms[0] - 1;
                         ˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1618:25: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        ci = _qlen - _mms[1] - 1;
                           ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1633:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                ci = _qlen - _mms[2] - 1;
                                   ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:1682:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        uint32_t icur = _qlen - i - 1; // current offset into _qry
                                 ˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:2475:37: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        uint64_t prehits = 0xffffffffffffffffllu)
                                           ^
./ebwt_search_backtrack.h:1934:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const unsigned int' [-Wshorten-64-to-32]
                qlen_ = min<uint32_t>(length(*qry_), qlen);
                        ˜˜˜           ^˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2033:13: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        offRev0_, offRev1_, offRev2_, offRev3_,
                                        ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2033:23: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        offRev0_, offRev1_, offRev2_, offRev3_,
                                                  ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2033:33: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        offRev0_, offRev1_, offRev2_, offRev3_,
                                                            ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2033:43: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        offRev0_, offRev1_, offRev2_, offRev3_,
                                                                      ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2034:16: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                        0, ftabChars, icost, iham, top, bot,
                                           ^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2060:12: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                offRev0_, offRev1_, offRev2_, offRev3_,
                                ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2060:22: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                offRev0_, offRev1_, offRev2_, offRev3_,
                                          ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2060:32: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                offRev0_, offRev1_, offRev2_, offRev3_,
                                                    ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2060:42: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                offRev0_, offRev1_, offRev2_, offRev3_,
                                                              ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1988:40: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const unsigned int' [-Wshorten-64-to-32]
                uint32_t m = min<uint32_t>(offRev0_, qlen_);
                             ˜˜˜                     ^˜˜˜˜
./ebwt_search_backtrack.h:2032:52: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        pm.rpool, pm.epool, pm.bpool.lastId(), qlen_,
                                                                               ^˜˜˜˜
./ebwt_search_backtrack.h:2059:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!b->init(pm.rpool, pm.epool, pm.bpool.lastId(), qlen_,
                            ˜                                              ^˜˜˜˜
./ebwt_search_backtrack.h:2144:27: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜                    ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2304:27: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜                    ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2337:32: warning: implicit conversion changes signedness: 'char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                        curRange_.refcs.push_back((char)br->edits_.get(i).chr);
                                        ˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2352:27: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜                    ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2356:27: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜                    ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2367:48: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        if(!pm.splitAndPrep(rand_, qlen_, qualLim_, depth3_,
                            ˜˜                                      ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2144:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜             ^˜˜˜˜
./ebwt_search_backtrack.h:2148:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        cur = qlen_ - depth - 1; // current offset into qry_
                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:2294:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        nedits = br->edits_.size();
                               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2304:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜             ^˜˜˜˜
./ebwt_search_backtrack.h:2336:60: warning: implicit conversion loses integer precision: 'unsigned long' to 'const value_type' (aka 'const unsigned int') [-Wshorten-64-to-32]
                                        curRange_.mms.push_back(qlen_ - br->edits_.get(i).pos - 1);
                                        ˜˜˜˜˜˜˜˜˜               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:2352:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜             ^˜˜˜˜
./ebwt_search_backtrack.h:2356:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                pm.curtail(br, qlen_, depth3_, qualOrder_);
                                ˜˜             ^˜˜˜˜
./ebwt_search_backtrack.h:2367:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!pm.splitAndPrep(rand_, qlen_, qualLim_, depth3_,
                            ˜˜                     ^˜˜˜˜
./ebwt_search_backtrack.h:2410:55: warning: implicit conversion loses integer precision: 'unsigned long' to 'const value_type' (aka 'const unsigned int') [-Wshorten-64-to-32]
                                curRange_.mms.push_back(qlen_ - seedRange_.mms[i] - 1);
                                ˜˜˜˜˜˜˜˜˜               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt_search_backtrack.h:2426:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t nedits = b->edits_.size();
                               ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2480:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t nedits = b->edits_.size();
                               ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2561:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                uint32_t ftabOff = (*qry_)[qlen_ - ftabChars];
                                                 ˜ ^˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2567:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        ftabOff |= (uint32_t)(*qry_)[qlen_-i];
                                                          ˜^
./ebwt_search_backtrack.h:2795:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                lowAtPos = qual[qlen - d - 1];
                                                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2803:61: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                        minCost += mmPenalty(maqPenalty_, phredCharToPhredQual(lowQual));
                                                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
./ebwt_search_backtrack.h:2810:30: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        minCost = (seed_ ? 3 : 2) << 14;
                                ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./ebwt_search_backtrack.h:2819:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                lowAtPos = qual[qlen - d - 1];
                                                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2827:61: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                        minCost += mmPenalty(maqPenalty_, phredCharToPhredQual(lowQual1));
                                                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2836:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                lowAtPos = qual[qlen - d - 1];
                                                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2854:61: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                        minCost += mmPenalty(maqPenalty_, phredCharToPhredQual(lowQual2_1));
                                                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2856:62: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                minCost += mmPenalty(maqPenalty_, phredCharToPhredQual(lowQual2_2));
                                                                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:2771:19: warning: implicit conversion loses integer precision: 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t qlen = seqan::length(qual);
                         ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search.cpp:14:
./ebwt.h:1675:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        while(cur < (upToSide * eh._sideSz)) {
                     ^˜˜˜˜˜˜˜ ˜
./ebwt.h:1737:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memset(seen, 0, 4 * seenLen);
        ˜˜˜˜˜˜          ˜˜^˜˜˜˜˜˜˜˜
./ebwt.h:1868:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
   x = x - ((x >> 1) & 0x5555555555555555llu);
                       ^
./ebwt.h:1869:13: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
   x = (x & 0x3333333333333333llu) + ((x >> 2) & 0x3333333333333333llu);
            ^
./ebwt.h:1869:50: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
   x = (x & 0x3333333333333333llu) + ((x >> 2) & 0x3333333333333333llu);
                                                 ^
./ebwt.h:1870:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
   x = (x + (x >> 4)) & 0x0F0F0F0F0F0F0F0Fllu;
                        ^
./ebwt.h:1883:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        uint64_t dwA  = dw &  0xAAAAAAAAAAAAAAAAllu;
                              ^
./ebwt.h:1884:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        uint64_t dwNA = dw & ˜0xAAAAAAAAAAAAAAAAllu;
                              ^
./ebwt.h:1902:8: warning: implicit conversion changes signedness: 'int' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
        tmp = pop64(tmp); // Gets 7.62% in profile
            ˜ ^˜˜˜˜˜˜˜˜˜
./ebwt.h:1918:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        uint64_t dwA  = dw &  0xAAAAAAAAAAAAAAAAllu;
                              ^
./ebwt.h:1919:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        uint64_t dwNA = dw & ˜0xAAAAAAAAAAAAAAAAllu;
                              ^
./ebwt.h:1920:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        arrs[0] += (32 - pop64((dwA >> 1) | dwNA));
                ˜˜  ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1921:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        arrs[1] += pop64(˜(dwA >> 1) & dwNA);
                ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1922:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        arrs[2] += pop64((dwA >> 1) & ˜dwNA);
                ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1923:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        arrs[3] += pop64((dwA >> 1) & dwNA);
                ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1945:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                cCnt += countInU64(c, *(uint64_t*)&side[i]);
                     ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3588:18: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        uint32_t nPat = readI32(in, switchEndian); // nPat
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:4193:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        int sideCur = eh._sideBwtSz - 1;
            ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:4354:28: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        sideCur = eh._sideBwtSz - 1;
                                ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:4437:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        eftabLen = eh._ftabChars*2;
                 ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
In file included from ebwt_search.cpp:22:
./range_cache.h:509:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                jumps = tops.size();
                                      ˜ ^˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search.cpp:25:
In file included from ./aligner.h:20:
./ref_aligner.h:306:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:306:44: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:311:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t anchor = 0llu;
                                  ^
./ref_aligner.h:312:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t buffw = 0llu;
                                 ^
./ref_aligner.h:315:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t clearMask = 0xffffffffffffffffllu;
                                     ^
./ref_aligner.h:321:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:346:27: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        anchor  = ((anchor  << 2llu) | c);
                                               ^
./ref_aligner.h:346:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor  = ((anchor  << 2llu) | c);
                                                     ˜ ^
./ref_aligner.h:347:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        buffw = ((buffw << 2llu) | r);
                                           ^
./ref_aligner.h:347:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:385:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                buffw = ((buffw << 2llu) | r);
                                                   ^
./ref_aligner.h:385:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:405:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        bufbw >>= 2llu;
                                                  ^
./ref_aligner.h:604:21: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.stratum = mms;
                                              ˜ ^˜˜
./ref_aligner.h:605:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.numMms = mms;
                                             ˜ ^˜˜
./ref_aligner.h:611:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc);
                                        ˜˜˜˜˜                 ^˜˜˜
./ref_aligner.h:650:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:650:44: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:651:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:657:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t anchor = 0llu;
                                  ^
./ref_aligner.h:658:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t buffw = 0llu;  // rotating ref sequence buffer
                                 ^
./ref_aligner.h:661:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t diffMask = 0llu;
                                    ^
./ref_aligner.h:664:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t clearMask = 0xffffffffffffffffllu;
                                     ^
./ref_aligner.h:700:29: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                        ^
./ref_aligner.h:700:37: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                                ^
./ref_aligner.h:702:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask <<= 2llu;
                                             ^
./ref_aligner.h:704:27: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        anchor  = ((anchor  << 2llu) | c);
                                               ^
./ref_aligner.h:704:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor  = ((anchor  << 2llu) | c);
                                                     ˜ ^
./ref_aligner.h:705:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        buffw = ((buffw << 2llu) | r);
                                           ^
./ref_aligner.h:705:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:748:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                buffw = ((buffw << 2llu) | r);
                                                   ^
./ref_aligner.h:748:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:767:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        bufbw >>= 2llu;
                                                  ^
./ref_aligner.h:778:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        if((diff & 0xffffffff00000000llu) &&
                                   ^
./ref_aligner.h:779:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x00000000ffffffffllu)) continue;
                                   ^
./ref_aligner.h:802:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos = nPos;
                                      ˜ ^˜˜˜
./ref_aligner.h:803:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc = "ACGT"[(int)ref[rir + nPos]];
                                                           ˜ ^˜˜˜
./ref_aligner.h:807:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos -= 16; }
                                           ^
./ref_aligner.h:807:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos -= 16; }
                                                                           ^
./ref_aligner.h:809:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos -=  8; }
                                           ^
./ref_aligner.h:809:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos -=  8; }
                                                                           ^
./ref_aligner.h:811:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos -=  4; }
                                           ^
./ref_aligner.h:811:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos -=  4; }
                                                                           ^
./ref_aligner.h:813:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos -=  2; }
                                           ^
./ref_aligner.h:813:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos -=  2; }
                                                                           ^
./ref_aligner.h:815:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0x3llu) == 0)        { mmpos--; }
                                           ^
./ref_aligner.h:894:27: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                range.refcs.push_back(refc);
                                ˜˜˜˜˜                 ^˜˜˜
./ref_aligner.h:1015:21: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.stratum = mms;
                                              ˜ ^˜˜
./ref_aligner.h:1016:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.numMms = mms;
                                             ˜ ^˜˜
./ref_aligner.h:1023:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc1);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1029:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc2);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1069:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:1069:44: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:1070:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:1076:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t anchor = 0llu;
                                  ^
./ref_aligner.h:1077:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t buffw = 0llu;  // rotating ref sequence buffer
                                 ^
./ref_aligner.h:1080:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t diffMask = 0llu;
                                    ^
./ref_aligner.h:1083:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t clearMask = 0xffffffffffffffffllu;
                                     ^
./ref_aligner.h:1126:29: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                        ^
./ref_aligner.h:1126:37: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                                ^
./ref_aligner.h:1128:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask <<= 2llu;
                                             ^
./ref_aligner.h:1130:27: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        anchor  = ((anchor  << 2llu) | c);
                                               ^
./ref_aligner.h:1130:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor  = ((anchor  << 2llu) | c);
                                                     ˜ ^
./ref_aligner.h:1131:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        buffw = ((buffw << 2llu) | r);
                                           ^
./ref_aligner.h:1131:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:1175:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                buffw = ((buffw << 2llu) | r);
                                                   ^
./ref_aligner.h:1175:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:1194:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        bufbw >>= 2llu;
                                                  ^
./ref_aligner.h:1205:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        if((diff & 0xfffff00000000000llu) &&
                                   ^
./ref_aligner.h:1206:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x00000ffffff00000llu) &&
                                   ^
./ref_aligner.h:1207:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x00000000000fffffllu)) continue;
                                   ^
./ref_aligner.h:1232:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos1 = nPos1;
                                       ˜ ^˜˜˜˜
./ref_aligner.h:1233:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc1 = "ACGT"[(int)ref[rir + nPos1]];
                                                            ˜ ^˜˜˜˜
./ref_aligner.h:1235:15: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        mmpos2 = nPos2;
                                               ˜ ^˜˜˜˜
./ref_aligner.h:1236:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        refc2 = "ACGT"[(int)ref[rir + nPos2]];
                                                                    ˜ ^˜˜˜˜
./ref_aligner.h:1242:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos1 -= 16; }
                                           ^
./ref_aligner.h:1242:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos1 -= 16; }
                                                                           ^
./ref_aligner.h:1244:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos1 -=  8; }
                                           ^
./ref_aligner.h:1244:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos1 -=  8; }
                                                                           ^
./ref_aligner.h:1246:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos1 -=  4; }
                                           ^
./ref_aligner.h:1246:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos1 -=  4; }
                                                                           ^
./ref_aligner.h:1248:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos1 -=  2; }
                                           ^
./ref_aligner.h:1248:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos1 -=  2; }
                                                                           ^
./ref_aligner.h:1250:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0x3llu) == 0)        { mmpos1--; }
                                           ^
./ref_aligner.h:1259:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        diff2 &= ˜(0xc000000000000000llu >> (uint64_t)((mmpos1+anchorCushion) << 1));
                                                   ^
./ref_aligner.h:1262:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffffffllu) == 0) { diff2 >>= 32llu; mmpos2 -= 16; }
                                                    ^
./ref_aligner.h:1262:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffffffllu) == 0) { diff2 >>= 32llu; mmpos2 -= 16; }
                                                                                     ^
./ref_aligner.h:1264:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffllu) == 0)     { diff2 >>= 16llu; mmpos2 -=  8; }
                                                    ^
./ref_aligner.h:1264:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffllu) == 0)     { diff2 >>= 16llu; mmpos2 -=  8; }
                                                                                     ^
./ref_aligner.h:1266:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffllu) == 0)       { diff2 >>= 8llu;  mmpos2 -=  4; }
                                                    ^
./ref_aligner.h:1266:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffllu) == 0)       { diff2 >>= 8llu;  mmpos2 -=  4; }
                                                                                     ^
./ref_aligner.h:1268:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xfllu) == 0)        { diff2 >>= 4llu;  mmpos2 -=  2; }
                                                    ^
./ref_aligner.h:1268:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xfllu) == 0)        { diff2 >>= 4llu;  mmpos2 -=  2; }
                                                                                     ^
./ref_aligner.h:1270:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0x3llu) == 0)        { mmpos2--; }
                                                    ^
./ref_aligner.h:1364:27: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                range.refcs.push_back(refc1);
                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1371:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc2);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1499:21: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.stratum = mms;
                                              ˜ ^˜˜
./ref_aligner.h:1500:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.numMms = mms;
                                             ˜ ^˜˜
./ref_aligner.h:1507:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc1);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1512:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc2);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1518:30: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                        range.refcs.push_back(refc3);
                                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1559:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:1559:44: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:1560:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:1566:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t anchor = 0llu;
                                  ^
./ref_aligner.h:1567:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t buffw = 0llu;  // rotating ref sequence buffer
                                 ^
./ref_aligner.h:1570:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t diffMask = 0llu;
                                    ^
./ref_aligner.h:1573:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t clearMask = 0xffffffffffffffffllu;
                                     ^
./ref_aligner.h:1621:29: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                        ^
./ref_aligner.h:1621:37: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                                ^
./ref_aligner.h:1623:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask <<= 2llu;
                                             ^
./ref_aligner.h:1625:27: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        anchor  = ((anchor  << 2llu) | c);
                                               ^
./ref_aligner.h:1625:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor  = ((anchor  << 2llu) | c);
                                                     ˜ ^
./ref_aligner.h:1626:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        buffw = ((buffw << 2llu) | r);
                                           ^
./ref_aligner.h:1626:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:1670:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                buffw = ((buffw << 2llu) | r);
                                                   ^
./ref_aligner.h:1670:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:1689:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        bufbw >>= 2llu;
                                                  ^
./ref_aligner.h:1700:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        if((diff & 0xffff000000000000llu) &&
                                   ^
./ref_aligner.h:1701:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x0000ffff00000000llu) &&
                                   ^
./ref_aligner.h:1702:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x00000000ffff0000llu) &&
                                   ^
./ref_aligner.h:1703:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x000000000000ffffllu)) continue;
                                   ^
./ref_aligner.h:1730:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos1 = nPos1;
                                       ˜ ^˜˜˜˜
./ref_aligner.h:1731:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc1 = "ACGT"[(int)ref[rir + nPos1]];
                                                            ˜ ^˜˜˜˜
./ref_aligner.h:1733:15: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        mmpos2 = nPos2;
                                               ˜ ^˜˜˜˜
./ref_aligner.h:1734:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        refc2 = "ACGT"[(int)ref[rir + nPos2]];
                                                                    ˜ ^˜˜˜˜
./ref_aligner.h:1736:16: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                mmpos3 = nPos3;
                                                       ˜ ^˜˜˜˜
./ref_aligner.h:1737:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                refc3 = "ACGT"[(int)ref[rir + nPos3]];
                                                                            ˜ ^˜˜˜˜
./ref_aligner.h:1744:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos1 -= 16; }
                                           ^
./ref_aligner.h:1744:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos1 -= 16; }
                                                                           ^
./ref_aligner.h:1746:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos1 -=  8; }
                                           ^
./ref_aligner.h:1746:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos1 -=  8; }
                                                                           ^
./ref_aligner.h:1748:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos1 -=  4; }
                                           ^
./ref_aligner.h:1748:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos1 -=  4; }
                                                                           ^
./ref_aligner.h:1750:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos1 -=  2; }
                                           ^
./ref_aligner.h:1750:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos1 -=  2; }
                                                                           ^
./ref_aligner.h:1752:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0x3llu) == 0)        { mmpos1--; }
                                           ^
./ref_aligner.h:1760:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        diff2 &= ˜(0xc000000000000000llu >> (uint64_t)((mmpos1 + anchorCushion) << 1));
                                                   ^
./ref_aligner.h:1763:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffffffllu) == 0) { diff2 >>= 32llu; mmpos2 -= 16; }
                                                    ^
./ref_aligner.h:1763:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffffffllu) == 0) { diff2 >>= 32llu; mmpos2 -= 16; }
                                                                                     ^
./ref_aligner.h:1765:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffllu) == 0)     { diff2 >>= 16llu; mmpos2 -=  8; }
                                                    ^
./ref_aligner.h:1765:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffllu) == 0)     { diff2 >>= 16llu; mmpos2 -=  8; }
                                                                                     ^
./ref_aligner.h:1767:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffllu) == 0)       { diff2 >>= 8llu;  mmpos2 -=  4; }
                                                    ^
./ref_aligner.h:1767:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffllu) == 0)       { diff2 >>= 8llu;  mmpos2 -=  4; }
                                                                                     ^
./ref_aligner.h:1769:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xfllu) == 0)        { diff2 >>= 4llu;  mmpos2 -=  2; }
                                                    ^
./ref_aligner.h:1769:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xfllu) == 0)        { diff2 >>= 4llu;  mmpos2 -=  2; }
                                                                                     ^
./ref_aligner.h:1771:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0x3llu) == 0)        { mmpos2--; }
                                                    ^
./ref_aligner.h:1790:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                diff3 &= ˜(0xc000000000000000llu >> (uint64_t)((mmpos2orig + anchorCushion) << 1));
                                                           ^
./ref_aligner.h:1792:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffffffffllu) == 0) { diff3 >>= 32llu; mmpos3 -= 16; }
                                                            ^
./ref_aligner.h:1792:52: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffffffffllu) == 0) { diff3 >>= 32llu; mmpos3 -= 16; }
                                                                                             ^
./ref_aligner.h:1794:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffffllu) == 0)     { diff3 >>= 16llu; mmpos3 -=  8; }
                                                            ^
./ref_aligner.h:1794:52: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffffllu) == 0)     { diff3 >>= 16llu; mmpos3 -=  8; }
                                                                                             ^
./ref_aligner.h:1796:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffllu) == 0)       { diff3 >>= 8llu;  mmpos3 -=  4; }
                                                            ^
./ref_aligner.h:1796:52: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffllu) == 0)       { diff3 >>= 8llu;  mmpos3 -=  4; }
                                                                                             ^
./ref_aligner.h:1798:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xfllu) == 0)        { diff3 >>= 4llu;  mmpos3 -=  2; }
                                                            ^
./ref_aligner.h:1798:52: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xfllu) == 0)        { diff3 >>= 4llu;  mmpos3 -=  2; }
                                                                                             ^
./ref_aligner.h:1800:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0x3llu) == 0)        { mmpos3--; }
                                                            ^
./ref_aligner.h:1909:27: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                range.refcs.push_back(refc1);
                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1916:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc2);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1923:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc3);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:2095:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[r]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜
./ref_aligner.h:2103:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.numMms = mms;
                                             ˜ ^˜˜
./ref_aligner.h:2191:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:2191:44: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:2192:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:2215:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t anchor = 0llu;
                                  ^
./ref_aligner.h:2216:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t buffw = 0llu;  // rotating ref sequence buffer
                                 ^
./ref_aligner.h:2219:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t clearMask = 0xffffffffffffffffllu;
                                     ^
./ref_aligner.h:2269:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        anchor = ((anchor << 2llu) | c);
                                             ^
./ref_aligner.h:2269:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor = ((anchor << 2llu) | c);
                                                   ˜ ^
./ref_aligner.h:2270:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        buffw = ((buffw << 2llu) | r);
                                           ^
./ref_aligner.h:2270:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:2325:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                buffw = ((buffw << 2llu) | r);
                                                   ^
./ref_aligner.h:2325:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:2344:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        bufbw >>= 2llu;
                                                  ^
./ref_aligner.h:2449:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:2460:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[rc]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:2511:19: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        range.numMms = mms;
                                     ˜ ^˜˜
./ref_aligner.h:2709:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[r]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜
./ref_aligner.h:2717:21: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.stratum = seedMms;
                                              ˜ ^˜˜˜˜˜˜
./ref_aligner.h:2718:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.numMms = mms;
                                             ˜ ^˜˜
./ref_aligner.h:2727:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc);
                                                ˜˜˜˜˜                 ^˜˜˜
./ref_aligner.h:2746:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc);
                                                ˜˜˜˜˜                 ^˜˜˜
./ref_aligner.h:2816:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:2816:44: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:2817:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:2840:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t anchor = 0llu;
                                  ^
./ref_aligner.h:2841:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t buffw = 0llu;  // rotating ref sequence buffer
                                 ^
./ref_aligner.h:2844:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t diffMask = 0llu;
                                    ^
./ref_aligner.h:2847:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t clearMask = 0xffffffffffffffffllu;
                                     ^
./ref_aligner.h:2903:29: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                        ^
./ref_aligner.h:2903:37: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                                ^
./ref_aligner.h:2905:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask <<= 2llu;
                                             ^
./ref_aligner.h:2907:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        anchor = ((anchor << 2llu) | c);
                                             ^
./ref_aligner.h:2907:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor = ((anchor << 2llu) | c);
                                                   ˜ ^
./ref_aligner.h:2908:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        buffw = ((buffw << 2llu) | r);
                                           ^
./ref_aligner.h:2908:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:2965:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                buffw = ((buffw << 2llu) | r);
                                                   ^
./ref_aligner.h:2965:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:2984:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        bufbw >>= 2llu;
                                                  ^
./ref_aligner.h:2995:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        if((diff & 0xffffffff00000000llu) &&
                                   ^
./ref_aligner.h:2996:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x00000000ffffffffllu)) continue;
                                   ^
./ref_aligner.h:3020:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos = nPos;
                                      ˜ ^˜˜˜
./ref_aligner.h:3022:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc = "ACGT"[(int)ref[rir + nPos]];
                                                           ˜ ^˜˜˜
./ref_aligner.h:3035:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos -= 16; }
                                           ^
./ref_aligner.h:3035:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos -= 16; }
                                                                           ^
./ref_aligner.h:3037:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos -=  8; }
                                           ^
./ref_aligner.h:3037:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos -=  8; }
                                                                           ^
./ref_aligner.h:3039:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos -=  4; }
                                           ^
./ref_aligner.h:3039:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos -=  4; }
                                                                           ^
./ref_aligner.h:3041:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos -=  2; }
                                           ^
./ref_aligner.h:3041:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos -=  2; }
                                                                           ^
./ref_aligner.h:3043:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0x3llu) == 0)        { mmpos--; }
                                           ^
./ref_aligner.h:3107:17: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                        char q = phredCharToPhredQual(quals[qoff]);
                                                             ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:3125:14: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        int mms = diffs; // start counting total mismatches
                            ˜˜˜   ^˜˜˜˜
./ref_aligner.h:3164:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:3175:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[rc]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:3228:19: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        range.numMms = mms;
                                     ˜ ^˜˜
./ref_aligner.h:3242:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc);
                                        ˜˜˜˜˜                 ^˜˜˜
./ref_aligner.h:3263:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc);
                                        ˜˜˜˜˜                 ^˜˜˜
./ref_aligner.h:3454:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[r]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜
./ref_aligner.h:3462:21: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.stratum = seedMms;
                                              ˜ ^˜˜˜˜˜˜
./ref_aligner.h:3463:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.numMms = mms;
                                             ˜ ^˜˜
./ref_aligner.h:3472:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc1);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:3477:30: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                        range.refcs.push_back(refc2);
                                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:3499:30: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                        range.refcs.push_back(refc2);
                                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:3503:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc1);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:3573:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:3573:44: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:3574:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:3597:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t anchor = 0llu;
                                  ^
./ref_aligner.h:3598:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t buffw = 0llu;  // rotating ref sequence buffer
                                 ^
./ref_aligner.h:3601:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t diffMask = 0llu;
                                    ^
./ref_aligner.h:3604:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t clearMask = 0xffffffffffffffffllu;
                                     ^
./ref_aligner.h:3671:29: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                        ^
./ref_aligner.h:3671:37: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                                ^
./ref_aligner.h:3673:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask <<= 2llu;
                                             ^
./ref_aligner.h:3675:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        anchor = ((anchor << 2llu) | c);
                                             ^
./ref_aligner.h:3675:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor = ((anchor << 2llu) | c);
                                                   ˜ ^
./ref_aligner.h:3676:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        buffw = ((buffw << 2llu) | r);
                                           ^
./ref_aligner.h:3676:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:3733:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                buffw = ((buffw << 2llu) | r);
                                                   ^
./ref_aligner.h:3733:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:3752:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        bufbw >>= 2llu;
                                                  ^
./ref_aligner.h:3763:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        if((diff & 0xf00f00f00f00f00fllu) &&
                                   ^
./ref_aligner.h:3764:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x0f00f00f00f00f00llu) &&
                                   ^
./ref_aligner.h:3765:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x00f00f00f00f00f0llu)) continue;
                                   ^
./ref_aligner.h:3766:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        if((diff & 0xc30c30c30c30c30cllu) &&
                                   ^
./ref_aligner.h:3767:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x30c30c30c30c30c3llu) &&
                                   ^
./ref_aligner.h:3768:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x0c30c30c30c30c30llu)) continue;
                                   ^
./ref_aligner.h:3794:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos1 = nPos1;
                                       ˜ ^˜˜˜˜
./ref_aligner.h:3795:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc1 = "ACGT"[(int)ref[rir + nPos1]];
                                                            ˜ ^˜˜˜˜
./ref_aligner.h:3806:15: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        mmpos2 = nPos2;
                                               ˜ ^˜˜˜˜
./ref_aligner.h:3807:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        refc2 = "ACGT"[(int)ref[rir + nPos2]];
                                                                    ˜ ^˜˜˜˜
./ref_aligner.h:3823:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos1 -= 16; }
                                           ^
./ref_aligner.h:3823:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos1 -= 16; }
                                                                           ^
./ref_aligner.h:3825:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos1 -=  8; }
                                           ^
./ref_aligner.h:3825:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos1 -=  8; }
                                                                           ^
./ref_aligner.h:3827:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos1 -=  4; }
                                           ^
./ref_aligner.h:3827:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos1 -=  4; }
                                                                           ^
./ref_aligner.h:3829:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos1 -=  2; }
                                           ^
./ref_aligner.h:3829:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos1 -=  2; }
                                                                           ^
./ref_aligner.h:3831:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0x3llu) == 0)        { mmpos1--; }
                                           ^
./ref_aligner.h:3851:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        diff2 &= ˜(0xc000000000000000llu >> (uint64_t)((savedMmpos1) << 1));
                                                   ^
./ref_aligner.h:3854:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffffffllu) == 0) { diff2 >>= 32llu; mmpos2 -= 16; }
                                                    ^
./ref_aligner.h:3854:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffffffllu) == 0) { diff2 >>= 32llu; mmpos2 -= 16; }
                                                                                     ^
./ref_aligner.h:3856:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffllu) == 0)     { diff2 >>= 16llu; mmpos2 -=  8; }
                                                    ^
./ref_aligner.h:3856:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffllu) == 0)     { diff2 >>= 16llu; mmpos2 -=  8; }
                                                                                     ^
./ref_aligner.h:3858:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffllu) == 0)       { diff2 >>= 8llu;  mmpos2 -=  4; }
                                                    ^
./ref_aligner.h:3858:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffllu) == 0)       { diff2 >>= 8llu;  mmpos2 -=  4; }
                                                                                     ^
./ref_aligner.h:3860:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xfllu) == 0)        { diff2 >>= 4llu;  mmpos2 -=  2; }
                                                    ^
./ref_aligner.h:3860:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xfllu) == 0)        { diff2 >>= 4llu;  mmpos2 -=  2; }
                                                                                     ^
./ref_aligner.h:3862:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0x3llu) == 0)        { mmpos2--; }
                                                    ^
./ref_aligner.h:3944:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:3961:14: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        int mms = diffs; // start counting total mismatches
                            ˜˜˜   ^˜˜˜˜
./ref_aligner.h:4000:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:4011:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[rc]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:4064:19: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        range.numMms = mms;
                                     ˜ ^˜˜
./ref_aligner.h:4078:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc1);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4089:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc2);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4111:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc1);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4122:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc2);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4322:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[r]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜
./ref_aligner.h:4330:21: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.stratum = seedMms;
                                              ˜ ^˜˜˜˜˜˜
./ref_aligner.h:4331:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                range.numMms = mms;
                                             ˜ ^˜˜
./ref_aligner.h:4340:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc1);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4345:30: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                        range.refcs.push_back(refc2);
                                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4350:31: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                                range.refcs.push_back(refc3);
                                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4374:31: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                                range.refcs.push_back(refc3);
                                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4379:30: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                        range.refcs.push_back(refc2);
                                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4383:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc1);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4453:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:4453:44: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:4454:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:4477:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t anchor = 0llu;
                                  ^
./ref_aligner.h:4478:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t buffw = 0llu;  // rotating ref sequence buffer
                                 ^
./ref_aligner.h:4481:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t diffMask = 0llu;
                                    ^
./ref_aligner.h:4484:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t clearMask = 0xffffffffffffffffllu;
                                     ^
./ref_aligner.h:4555:29: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                        ^
./ref_aligner.h:4555:37: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask = (diffMask << 2llu) | 1llu;
                                                                ^
./ref_aligner.h:4557:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                diffMask <<= 2llu;
                                             ^
./ref_aligner.h:4559:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        anchor = ((anchor << 2llu) | c);
                                             ^
./ref_aligner.h:4559:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor = ((anchor << 2llu) | c);
                                                   ˜ ^
./ref_aligner.h:4560:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        buffw = ((buffw << 2llu) | r);
                                           ^
./ref_aligner.h:4560:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:4617:24: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                buffw = ((buffw << 2llu) | r);
                                                   ^
./ref_aligner.h:4617:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:4636:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        bufbw >>= 2llu;
                                                  ^
./ref_aligner.h:4647:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        if((diff & 0xf000f000f000f000llu) &&
                                   ^
./ref_aligner.h:4648:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x0f000f000f000f00llu) &&
                                   ^
./ref_aligner.h:4649:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x00f000f000f000f0llu) &&
                                   ^
./ref_aligner.h:4650:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x000f000f000f000fllu)) continue;
                                   ^
./ref_aligner.h:4651:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        if((diff & 0xc003c003c003c003llu) &&
                                   ^
./ref_aligner.h:4652:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x3c003c003c003c00llu) &&
                                   ^
./ref_aligner.h:4653:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x03c003c003c003c0llu) &&
                                   ^
./ref_aligner.h:4654:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                           (diff & 0x003c003c003c003cllu)) continue;
                                   ^
./ref_aligner.h:4682:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos1 = nPos1;
                                       ˜ ^˜˜˜˜
./ref_aligner.h:4683:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc1 = "ACGT"[(int)ref[rir + nPos1]];
                                                            ˜ ^˜˜˜˜
./ref_aligner.h:4694:15: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        mmpos2 = nPos2;
                                               ˜ ^˜˜˜˜
./ref_aligner.h:4695:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        refc2 = "ACGT"[(int)ref[rir + nPos2]];
                                                                    ˜ ^˜˜˜˜
./ref_aligner.h:4706:16: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                mmpos3 = nPos3;
                                                       ˜ ^˜˜˜˜
./ref_aligner.h:4707:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                refc3 = "ACGT"[(int)ref[rir + nPos3]];
                                                                            ˜ ^˜˜˜˜
./ref_aligner.h:4723:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos1 -= 16; }
                                           ^
./ref_aligner.h:4723:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffffffllu) == 0) { diff >>= 32llu; mmpos1 -= 16; }
                                                                           ^
./ref_aligner.h:4725:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos1 -=  8; }
                                           ^
./ref_aligner.h:4725:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffffllu) == 0)     { diff >>= 16llu; mmpos1 -=  8; }
                                                                           ^
./ref_aligner.h:4727:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos1 -=  4; }
                                           ^
./ref_aligner.h:4727:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xffllu) == 0)       { diff >>= 8llu;  mmpos1 -=  4; }
                                                                           ^
./ref_aligner.h:4729:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos1 -=  2; }
                                           ^
./ref_aligner.h:4729:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0xfllu) == 0)        { diff >>= 4llu;  mmpos1 -=  2; }
                                                                           ^
./ref_aligner.h:4731:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                if((diff & 0x3llu) == 0)        { mmpos1--; }
                                           ^
./ref_aligner.h:4751:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        diff2 &= ˜(0xc000000000000000llu >> (uint64_t)((savedMmpos1) << 1));
                                                   ^
./ref_aligner.h:4755:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffffffllu) == 0) { diff2 >>= 32llu; mmpos2 -= 16; }
                                                    ^
./ref_aligner.h:4755:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffffffllu) == 0) { diff2 >>= 32llu; mmpos2 -= 16; }
                                                                                     ^
./ref_aligner.h:4757:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffllu) == 0)     { diff2 >>= 16llu; mmpos2 -=  8; }
                                                    ^
./ref_aligner.h:4757:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffffllu) == 0)     { diff2 >>= 16llu; mmpos2 -=  8; }
                                                                                     ^
./ref_aligner.h:4759:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffllu) == 0)       { diff2 >>= 8llu;  mmpos2 -=  4; }
                                                    ^
./ref_aligner.h:4759:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xffllu) == 0)       { diff2 >>= 8llu;  mmpos2 -=  4; }
                                                                                     ^
./ref_aligner.h:4761:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xfllu) == 0)        { diff2 >>= 4llu;  mmpos2 -=  2; }
                                                    ^
./ref_aligner.h:4761:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0xfllu) == 0)        { diff2 >>= 4llu;  mmpos2 -=  2; }
                                                                                     ^
./ref_aligner.h:4763:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                        if((diff2 & 0x3llu) == 0)        { mmpos2--; }
                                                    ^
./ref_aligner.h:4792:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                diff3 &= ˜(0xc000000000000000llu >> (uint64_t)((savedMmpos2) << 1));
                                                           ^
./ref_aligner.h:4795:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffffffffllu) == 0) { diff3 >>= 32llu; mmpos3 -= 16; }
                                                            ^
./ref_aligner.h:4795:52: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffffffffllu) == 0) { diff3 >>= 32llu; mmpos3 -= 16; }
                                                                                             ^
./ref_aligner.h:4797:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffffllu) == 0)     { diff3 >>= 16llu; mmpos3 -=  8; }
                                                            ^
./ref_aligner.h:4797:52: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffffllu) == 0)     { diff3 >>= 16llu; mmpos3 -=  8; }
                                                                                             ^
./ref_aligner.h:4799:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffllu) == 0)       { diff3 >>= 8llu;  mmpos3 -=  4; }
                                                            ^
./ref_aligner.h:4799:52: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xffllu) == 0)       { diff3 >>= 8llu;  mmpos3 -=  4; }
                                                                                             ^
./ref_aligner.h:4801:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xfllu) == 0)        { diff3 >>= 4llu;  mmpos3 -=  2; }
                                                            ^
./ref_aligner.h:4801:52: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0xfllu) == 0)        { diff3 >>= 4llu;  mmpos3 -=  2; }
                                                                                             ^
./ref_aligner.h:4803:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                                if((diff3 & 0x3llu) == 0)        { mmpos3--; }
                                                            ^
./ref_aligner.h:4902:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:4919:14: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        int mms = diffs; // start counting total mismatches
                            ˜˜˜   ^˜˜˜˜
./ref_aligner.h:4958:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:4969:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[rc]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:5022:19: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        range.numMms = mms;
                                     ˜ ^˜˜
./ref_aligner.h:5036:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc1);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:5046:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc2);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:5057:30: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                        range.refcs.push_back(refc3);
                                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:5080:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc1);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:5090:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc2);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:5101:30: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                        range.refcs.push_back(refc3);
                                                        ˜˜˜˜˜                 ^˜˜˜˜
In file included from ebwt_search.cpp:25:
./aligner.h:989:29: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                uint32_t insDiff = maxins - minins;
                         ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./aligner.h:991:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        end = toff + maxins;
                                   ˜ ^˜˜˜˜˜
./aligner.h:1010:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                begin = toff + alen - maxins;
                                                    ˜ ^˜˜˜˜˜
./aligner.h:1017:44: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                end = min<uint32_t>(end, toff + alen - minins + qlen - 1);
                                                                     ˜ ^˜˜˜˜˜
./aligner.h:1930:29: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                uint32_t insDiff = maxins - minins;
                         ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./aligner.h:1932:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        end = toff + maxins;
                                   ˜ ^˜˜˜˜˜
./aligner.h:1951:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                begin = toff + alen - maxins;
                                                    ˜ ^˜˜˜˜˜
./aligner.h:1958:44: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                end = min<uint32_t>(end, toff + alen - minins + qlen - 1);
                                                                     ˜ ^˜˜˜˜˜
In file included from ebwt_search.cpp:29:
./aligner_seed_mm.h:92:22: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, true,  qualCutoff_, true, verbose_, quiet_,
                                                 ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:95:22: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, false, qualCutoff_, true, verbose_, quiet_,
                                                 ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:124:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:127:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:130:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:166:19: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw, qualCutoff_, true,  verbose_, quiet_,
                                              ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:169:19: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw, qualCutoff_, true,  verbose_, quiet_,
                                              ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:172:19: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_,
                                              ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:219:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_);
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:221:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_);
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:223:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_, 0, true,  maqPenalty_, qualOrder_, metrics_);
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:225:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_, 2,  false, maqPenalty_, qualOrder_, metrics_);
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:269:19: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw, qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_);
                                              ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:271:19: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw, qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_);
                                              ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:273:19: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 0, true,  maqPenalty_, qualOrder_, metrics_);
                                              ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:275:19: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 2,  false, maqPenalty_, qualOrder_, metrics_);
                                              ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:332:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:339:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:342:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:349:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:353:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:357:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:425:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:432:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:435:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:442:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:445:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                 ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:449:20: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_,
                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:670:88: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        refAligner = new Seed0RefAligner<String<Dna5> >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_);
                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                    ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:672:88: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        refAligner = new Seed1RefAligner<String<Dna5> >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_);
                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                    ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:674:88: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        refAligner = new Seed2RefAligner<String<Dna5> >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_);
                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                    ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:676:88: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        refAligner = new Seed3RefAligner<String<Dna5> >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_);
                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                    ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:713:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, true, verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:730:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, true, verbose_, quiet_, halfAndHalf,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:747:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, true, verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:764:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, true, verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:783:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:786:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:789:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:827:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:830:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:833:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:871:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:874:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:877:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:915:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:918:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:921:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_,
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:961:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:963:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:965:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_, 0, true,  maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:967:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_, 2,  false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1000:22: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                 ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1014:22: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_, 3,  true,  maqPenalty_, qualOrder_);
                                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1050:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1052:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1054:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_, 0, true,  maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1056:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_, 2,  false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1090:22: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                 ebwtBw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1104:22: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_, 3,  true,  maqPenalty_, qualOrder_);
                                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1140:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1142:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1144:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_, 0, true,  maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1146:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_, 2,  false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1180:22: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1194:22: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                 ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_, 3,  true,  maqPenalty_, qualOrder_);
                                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1230:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1232:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1234:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                         ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_, 0, true,  maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1236:21: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        &ebwtFw_, fw,  qualCutoff_, false, verbose_, quiet_, 2,  false, maqPenalty_, qualOrder_);
                                                       ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1270:22: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                &ebwtFw_, fw,  qualCutoff_, true,  verbose_, quiet_, 0, false, maqPenalty_, qualOrder_);
                                                               ^˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:1284:22: warning: implicit conversion changes signedness: 'const int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                 ebwtBw_, fw,  qualCutoff_, false, verbose_, quiet_, 3,  true,  maqPenalty_, qualOrder_);
                                                               ^˜˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:682:25: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        suppressOuts.set(ii-1);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜     ˜˜^˜
ebwt_search.cpp:732:21: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                prefetchWidth = parseInt(1, "--prewidth must be at least 1");
                                              ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1097:56: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patsrcFact = new RandomPatternSourcePerThreadFactory(numRandomReads, lenRandomReads, nthreads, tid);
                                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1171:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                0xffffffff,     // max backtracks (no max)
                ^˜˜˜˜˜˜˜˜˜
In file included from ebwt_search.cpp:1184:
./search_exact.c:8:18: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t plen = length(patsrc->bufa().patFw);
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1205:42: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
                              ˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜
ebwt_search.cpp:1205:76: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
                              ˜˜˜˜˜˜˜˜˜                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
ebwt_search.cpp:1225:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seed);
                        ^˜˜˜
ebwt_search.cpp:1255:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seed);
                        ^˜˜˜
ebwt_search.cpp:1318:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<tthread::thread*> threads(nthreads);
                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:1319:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<int> tids(nthreads);
                       ˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:1326:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        tids[i] = i+1;
                        ˜˜˜˜ ^
ebwt_search.cpp:1328:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(exactSearchWorkerStateful, (void*)&tids[i]);
                                ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1328:106: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(exactSearchWorkerStateful, (void*)&tids[i]);
                                                                                                    ˜˜˜˜ ^
ebwt_search.cpp:1330:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(exactSearchWorker, (void*)&tids[i]);
                                ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1330:98: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(exactSearchWorker, (void*)&tids[i]);
                                                                                            ˜˜˜˜ ^
ebwt_search.cpp:1335:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                    threads[i]->join();
                    ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1374:42: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
                              ˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜
ebwt_search.cpp:1374:76: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
                              ˜˜˜˜˜˜˜˜˜                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
ebwt_search.cpp:1395:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seed);
                        ^˜˜˜
ebwt_search.cpp:1425:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seed);
                        ^˜˜˜
ebwt_search.cpp:1467:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                0xffffffff,     // max backtracks (no max)
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1480:19: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t plen = length(patFw);
                         ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1533:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<tthread::thread*> threads(nthreads);
                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:1534:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<int> tids(nthreads);
                       ˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:1541:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        tids[i] = i+1;
                        ˜˜˜˜ ^
ebwt_search.cpp:1543:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(mismatchSearchWorkerFullStateful, (void*)&tids[i]);
                                ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1543:113: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(mismatchSearchWorkerFullStateful, (void*)&tids[i]);
                                                                                                           ˜˜˜˜ ^
ebwt_search.cpp:1545:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(mismatchSearchWorkerFull, (void*)&tids[i]);
                                ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1545:105: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(mismatchSearchWorkerFull, (void*)&tids[i]);
                                                                                                   ˜˜˜˜ ^
ebwt_search.cpp:1549:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                    threads[i]->join();
                    ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1671:42: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
                              ˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜
ebwt_search.cpp:1671:76: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
                              ˜˜˜˜˜˜˜˜˜                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
ebwt_search.cpp:1692:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seed);
                        ^˜˜˜
ebwt_search.cpp:1723:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seed);
                        ^˜˜˜
ebwt_search.cpp:1752:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                0xffffffff,     // max backtracks (no limit)
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1766:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                0xffffffff,     // max backtracks (no limit)
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1780:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                0xffffffff,     // max backtracks (no limit)
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1794:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                0xffffffff,     // max backtracks (no limit)
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1809:19: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t plen = length(patFw);
                         ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1864:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<tthread::thread*> threads(nthreads);
                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:1865:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<int> tids(nthreads);
                       ˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:1871:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        tids[i] = i+1;
                        ˜˜˜˜ ^
ebwt_search.cpp:1873:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                            threads[i] = new tthread::thread(twoOrThreeMismatchSearchWorkerStateful, (void*)&tids[i]);
                            ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1873:115: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                            threads[i] = new tthread::thread(twoOrThreeMismatchSearchWorkerStateful, (void*)&tids[i]);
                                                                                                             ˜˜˜˜ ^
ebwt_search.cpp:1875:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                            threads[i] = new tthread::thread(twoOrThreeMismatchSearchWorkerFull, (void *)&tids[i]);
                            ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1875:112: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                            threads[i] = new tthread::thread(twoOrThreeMismatchSearchWorkerFull, (void *)&tids[i]);
                                                                                                          ˜˜˜˜ ^
ebwt_search.cpp:1879:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                    threads[i]->join();
                    ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1931:10: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                qualCutoff,            // qualThresh
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1944:10: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                qualCutoff,            // qualThresh
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1959:10: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                qualCutoff,            // qualThresh
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1974:10: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                qualCutoff,            // qualThresh (none)
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1976:10: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                seedMms,               // report partials (up to seedMms mms)
                ^˜˜˜˜˜˜
ebwt_search.cpp:1989:10: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                qualCutoff,            // qualThresh (none)
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:1991:10: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                seedMms,               // reportPartials (do)
                ^˜˜˜˜˜˜
ebwt_search.cpp:2005:10: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                qualCutoff, // qualThresh
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:2020:10: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                qualCutoff, // qualThresh
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:2037:10: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                qualCutoff, // qualThresh
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:2052:10: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                qualCutoff, // qualThresh
                ^˜˜˜˜˜˜˜˜˜
ebwt_search.cpp:2070:16: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                uint32_t s = seedLen;
                         ˜   ^˜˜˜˜˜˜
In file included from ebwt_search.cpp:2077:
./search_seeded_phase1.c:25:35: warning: implicit conversion changes signedness: 'int' to 'const unsigned long' [-Wsign-conversion]
                size_t slen = min<size_t>(plen, seedLen);
                              ˜˜˜               ^˜˜˜˜˜˜
In file included from ebwt_search.cpp:2079:
./search_seeded_phase3.c:103:15: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        btf3.setQlen(seedLen); // just look at the seed
        ˜˜˜˜         ^˜˜˜˜˜˜
ebwt_search.cpp:2073:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const unsigned int' [-Wshorten-64-to-32]
                uint32_t qs = min<uint32_t>(plen, s);
                              ˜˜˜           ^˜˜˜
In file included from ebwt_search.cpp:2077:
./search_seeded_phase1.c:51:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                btf1.setOffs(0, plen, plen, plen, plen, plen);
                ˜˜˜˜            ^˜˜˜
./search_seeded_phase1.c:51:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                btf1.setOffs(0, plen, plen, plen, plen, plen);
                ˜˜˜˜                  ^˜˜˜
./search_seeded_phase1.c:51:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                btf1.setOffs(0, plen, plen, plen, plen, plen);
                ˜˜˜˜                        ^˜˜˜
./search_seeded_phase1.c:51:37: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                btf1.setOffs(0, plen, plen, plen, plen, plen);
                ˜˜˜˜                              ^˜˜˜
./search_seeded_phase1.c:51:43: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                btf1.setOffs(0, plen, plen, plen, plen, plen);
                ˜˜˜˜                                    ^˜˜˜
ebwt_search.cpp:2104:42: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
                              ˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜
ebwt_search.cpp:2104:76: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
                              ˜˜˜˜˜˜˜˜˜                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
ebwt_search.cpp:2115:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seedMms,
                        ^˜˜˜˜˜˜
ebwt_search.cpp:2116:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seedLen,
                        ^˜˜˜˜˜˜
ebwt_search.cpp:2133:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seed,
                        ^˜˜˜
ebwt_search.cpp:2142:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seedMms,
                        ^˜˜˜˜˜˜
ebwt_search.cpp:2143:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seedLen,
                        ^˜˜˜˜˜˜
ebwt_search.cpp:2169:4: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        seed);
                        ^˜˜˜
ebwt_search.cpp:2242:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<tthread::thread*> threads(nthreads);
                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:2243:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<int> tids(nthreads);
                       ˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:2258:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        tids[i] = i+1;
                        ˜˜˜˜ ^
ebwt_search.cpp:2260:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(seededQualSearchWorkerFullStateful, (void*)&tids[i]);
                                ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:2260:115: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(seededQualSearchWorkerFullStateful, (void*)&tids[i]);
                                                                                                             ˜˜˜˜ ^
ebwt_search.cpp:2262:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(seededQualSearchWorkerFull, (void*)&tids[i]);
                                ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:2262:107: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(seededQualSearchWorkerFull, (void*)&tids[i]);
                                                                                                     ˜˜˜˜ ^
ebwt_search.cpp:2266:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                    threads[i]->join();
                    ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:2287:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        return new FastaPatternSource (seed, reads, quals, color,
                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜  ^˜˜˜
ebwt_search.cpp:2296:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                       seed, reads, fastaContLen,
                                                       ^˜˜˜
ebwt_search.cpp:2301:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        return new RawPatternSource   (seed, reads, color,
                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜    ^˜˜˜
ebwt_search.cpp:2307:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        return new FastqPatternSource (seed, reads, color,
                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜  ^˜˜˜
ebwt_search.cpp:2315:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        return new TabbedPatternSource(seed, reads, color,
                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
ebwt_search.cpp:2321:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        return new VectorPatternSource(seed, reads, color,
                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
ebwt_search.cpp:2327:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        return new RandomPatternSource(seed, 2000000, lenRandomReads,
                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
ebwt_search.cpp:2483:52: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patsrc = new PairedSoloPatternSource(patsrcs_ab, seed);
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜             ^˜˜˜
ebwt_search.cpp:2485:62: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patsrc = new PairedDualPatternSource(patsrcs_a, patsrcs_b, seed);
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                       ^˜˜˜
ebwt_search.cpp:2577:27: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                                os.erase(os.begin() + i);
                                         ˜˜           ^
ebwt_search.cpp:2777:48: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                                 << ", " << sizeof(long) << ", " << sizeof(long long)
                                                                           ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:77:16: note: in instantiation of function template specialization 'seqan::length<char, seqan::Alloc<void> >' requested here
        size_t plen = length(path);
                      ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./alphabet.h:144:19: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >' requested here
        size_t readLen = seqan::length(read);
                         ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<char>' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<char>' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<char>' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<char>' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<char, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<char, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<char, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:278:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<char, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(name, sz);
                ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<seqan::SimpleType<unsigned char, seqan::_Dna5>, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:283:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(seq, sz);
                ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:90:
SeqAn-1.1/seqan/basic/basic_iterator_adapt_std.h:307:67: warning: implicit conversion changes signedness: 'unsigned long' to 'const difference_type' (aka 'const long') [-Wsign-conversion]
        return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) + right);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:764:76: note: in instantiation of function template specialization 'seqan::operator+<const std::basic_string<char>, unsigned long>' requested here
                        arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
                                                                                                ^
SeqAn-1.1/seqan/sequence/string_base.h:812:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, const std::basic_string<char> >' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:737:2: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char>, seqan::TagGenerous_>' requested here
        assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:70:3: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char> >' requested here
                assign(*this, source);
                ^
./pat.h:1391:17: note: in instantiation of function template specialization 'seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >::String<std::basic_string<char> >' requested here
                        v_.push_back(s);
                                     ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:323:17: warning: implicit conversion loses integer precision: 'const unsigned int' to 'unsigned char' [-Wconversion]
        target.value = source;
                     ˜ ^˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:82:3: note: in instantiation of function template specialization 'seqan::assign<unsigned char, seqan::_Dna, unsigned int>' requested here
                assign(*this, other);
                ^
SeqAn-1.1/seqan/sequence/string_packed.h:958:9: note: in instantiation of function template specialization 'seqan::SimpleType<unsigned char, seqan::_Dna>::SimpleType<unsigned int>' requested here
        return (value(hostIterator(me)) >> _bitpos(me)) & _PackedConsts<TContainer>::VALUE_MASK;
               ^
SeqAn-1.1/seqan/basic/basic_proxy.h:242:9: note: in instantiation of function template specialization 'seqan::getValue<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void> >' requested here
        return getValue(iter(me));
               ^
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:345:17: note: in instantiation of function template specialization 'seqan::getValue<seqan::IteratorProxy<seqan::Iter<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Packed<seqan::Alloc<void> > > > >' requested here
        target.value = getValue(source);
                       ^
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:82:3: note: in instantiation of function template specialization 'seqan::assign<unsigned char, seqan::_Dna, seqan::IteratorProxy<seqan::Iter<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Packed<seqan::Alloc<void> > > > >' requested here
                assign(*this, other);
                ^
./multikey_qsort.h:793:18: note: in instantiation of function template specialization 'seqan::SimpleType<unsigned char, seqan::_Dna>::SimpleType<seqan::Proxy<seqan::IteratorProxy<seqan::Iter<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Packed<seqan::Alloc<void> > > > > >' requested here
        return (uint8_t)(Dna)t[off];
                        ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<unsigned int, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./blockwise_sa.h:353:28: note: in instantiation of function template specialization 'seqan::length<unsigned int, seqan::Alloc<void> >' requested here
        uint32_t slen = (uint32_t)seqan::length(bucket);
                                  ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:9: warning: implicit conversion changes signedness: 'typename Difference<Iter<const String<SimpleType<unsigned char, _Dna>, Packed<Alloc<void> > >, Packed<Alloc<void> > > >::Type' (aka 'long') to 'typename Size<const String<SimpleType<unsigned char, _Dna>, Packed<Alloc<void> > > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./blockwise_sa.h:354:27: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >' requested here
        uint32_t len = (uint32_t)seqan::length(t);
                                 ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:431:23: warning: implicit conversion changes signedness: 'int' to 'TPosition' (aka 'unsigned long') [-Wsign-conversion]
        return TIterator(me, pos_);
               ˜˜˜˜˜˜˜˜˜     ^˜˜˜
SeqAn-1.1/seqan/sequence/string_packed.h:450:9: note: in instantiation of function template specialization 'seqan::iter<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, int, seqan::TagStandard_>' requested here
        return iter(me, 0, tag_);
               ^
SeqAn-1.1/seqan/sequence/string_base.h:181:31: note: in instantiation of function template specialization 'seqan::begin<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, seqan::TagStandard_>' requested here
        return end(me, Standard()) - begin(me, Standard());
                                     ^
./blockwise_sa.h:354:27: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >' requested here
        uint32_t len = (uint32_t)seqan::length(t);
                                 ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:1237:24: warning: implicit conversion changes signedness: 'unsigned long' to 'typename Difference<Iter<const String<SimpleType<unsigned char, _Dna>, Packed<Alloc<void> > >, Packed<Alloc<void> > > >::Type' (aka 'long') [-Wsign-conversion]
        return position(left) - position(right);
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:181:29: note: in instantiation of function template specialization 'seqan::operator-<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void> >' requested here
        return end(me, Standard()) - begin(me, Standard());
                                   ^
./blockwise_sa.h:354:27: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >' requested here
        uint32_t len = (uint32_t)seqan::length(t);
                                 ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:906:88: warning: implicit conversion changes signedness: 'long' to 'typename Position<const Iter<const String<SimpleType<unsigned char, _Dna>, Packed<Alloc<void> > >, Packed<Alloc<void> > > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return (hostIterator(me) - begin(host_)) * _PackedConsts<TContainer>::VALUES_PER_WORD + _bitpos(me) / _PackedConsts<TContainer>::BITS_PER_VALUE;
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_packed.h:1237:9: note: in instantiation of function template specialization 'seqan::position<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void> >' requested here
        return position(left) - position(right);
               ^
SeqAn-1.1/seqan/sequence/string_base.h:181:29: note: in instantiation of function template specialization 'seqan::operator-<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::Alloc<void> >' requested here
        return end(me, Standard()) - begin(me, Standard());
                                   ^
./blockwise_sa.h:354:27: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >' requested here
        uint32_t len = (uint32_t)seqan::length(t);
                                 ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:360:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                mkeyQSortSufDcU8(t, t, len, s, slen, *_dc,
                ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                        ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                   ^
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1079:10: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1098:30: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1108:30: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:72: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜
./multikey_qsort.h:1064:65: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                       ^˜˜˜˜
./multikey_qsort.h:1064:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                              ^˜˜
./multikey_qsort.h:1073:65: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                       ^˜˜˜˜
./multikey_qsort.h:1073:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                              ^˜˜
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:208:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                if     (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:209:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:210:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:11: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                        ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:19: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                           ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:23: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                    ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1078:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:38: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                   ^
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:46: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                      ˜˜˜˜˜^˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1078:2: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:217:31: note: expanded from macro 'CHOOSE_AND_SWAP_PIVOT'
#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:211:50: note: expanded from macro 'CHOOSE_AND_SWAP_SMART_PIVOT'
                else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
                                                               ^˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1079:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1079:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1079:32: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1098:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1098:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1098:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:1108:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:54: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
./multikey_qsort.h:1108:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./multikey_qsort.h:186:63: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                              ^
./multikey_qsort.h:1108:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:186:67: note: expanded from macro 'CHAR_AT_SUF_U8'
#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
                                                                  ^
./multikey_qsort.h:748:14: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        size_t a = (rand() % n) + begin; // choose pivot between begin and end
                    ^˜˜˜˜˜ ˜
./multikey_qsort.h:1062:3: note: in instantiation of function template specialization 'qsortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                qsortSufDcU8<T1,T2>(seqanHost, host, hlen, s, slen, dc, begin, end, sanityCheck);
                ^
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:360:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                mkeyQSortSufDcU8(t, t, len, s, slen, *_dc,
                ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:977:39: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                               0xffffffff, begin, end);
                                                           ^˜˜˜˜
./multikey_qsort.h:1070:3: note: in instantiation of function template specialization 'bucketSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                bucketSortSufDcU8(seqanHost, host, hlen, s, slen, dc,
                ^
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:360:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                mkeyQSortSufDcU8(t, t, len, s, slen, *_dc,
                ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:977:46: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                               0xffffffff, begin, end);
                                                                  ^˜˜
./multikey_qsort.h:982:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t off = depth+s[i];
                         ˜˜˜   ˜˜˜˜˜^˜˜˜˜
./multikey_qsort.h:992:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        uint32_t cur = begin + cnts[0];
                 ˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./multikey_qsort.h:1000:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cur = begin;
            ˜ ^˜˜˜˜
./multikey_qsort.h:852:41: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                               0xffffffff, begin, end);
                                                                           ^˜˜˜˜
./multikey_qsort.h:973:3: note: in instantiation of function template specialization 'selectionSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                selectionSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi,
                ^
./multikey_qsort.h:1070:3: note: in instantiation of function template specialization 'bucketSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                bucketSortSufDcU8(seqanHost, host, hlen, s, slen, dc,
                ^
./multikey_qsort.h:687:2: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
        mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
        ^
./blockwise_sa.h:360:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                mkeyQSortSufDcU8(t, t, len, s, slen, *_dc,
                ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
./multikey_qsort.h:852:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                               0xffffffff, begin, end);
                                                                                  ^˜˜
./multikey_qsort.h:856:20: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        v = off - depth + 1;
                          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./multikey_qsort.h:863:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t targ = i;
                         ˜˜˜˜   ^
./multikey_qsort.h:864:28: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t targoff = depth + s[i];
                         ˜˜˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:867:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        uint32_t joff = depth + s[j];
                                 ˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜
./multikey_qsort.h:883:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        targ = j;
                                             ˜ ^
./multikey_qsort.h:899:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                targ = j;
                                                     ˜ ^
./multikey_qsort.h:916:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        targ = j;
                                             ˜ ^
./multikey_qsort.h:937:38: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                       0xffffffff, begin, end);
                                                   ^˜˜˜˜
./multikey_qsort.h:937:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                       0xffffffff, begin, end);
                                                          ^˜˜
./multikey_qsort.h:326:35: warning: implicit conversion loses integer precision: 'unsigned long' to 'const unsigned int' [-Wshorten-64-to-32]
        upper = min<uint32_t>(upper, slen-1);
                ˜˜˜                  ˜˜˜˜^˜
./multikey_qsort.h:688:18: note: in instantiation of function template specialization 'sanityCheckOrderedSufs<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
        if(sanityCheck) sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff);
                        ^
./blockwise_sa.h:360:3: note: in instantiation of function template specialization 'mkeyQSortSufDcU8<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > >, seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<seqan::Alloc<void> > > >' requested here
                mkeyQSortSufDcU8(t, t, len, s, slen, *_dc,
                ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:415:50: warning: implicit conversion changes signedness: 'int' to 'typename Size<String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        if (old_capacity >= (TSize)new_capacity) return new_capacity;
                                                 ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/sequence_interface.h:1325:9: note: in instantiation of function template specialization 'seqan::reserve<QueryMutation, void, int, seqan::TagExact_>' requested here
        return reserve(me, new_capacity, typename DefaultOverflowExplicit<T>::Type());
               ^
./ebwt_search_util.h:315:3: note: in instantiation of function template specialization 'seqan::reserve<seqan::String<QueryMutation, seqan::Alloc<void> >, int>' requested here
                reserve(muts, 4);
                ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:418:94: warning: implicit conversion changes signedness: 'int' to 'typename Size<String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        typename Value< String<TValue, Alloc<TSpec> > >::Type * old_array = _reallocateStorage(seq, new_capacity, tag);
                                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_alloc.h:430:9: warning: implicit conversion changes signedness: 'int' to 'typename Size<String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return new_capacity;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search.cpp:14:
./ebwt.h:2091:59: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
        if(l._sideByteOff <= _zEbwtByteOff && l._sideByteOff + l._by >= _zEbwtByteOff) {
                                                             ˜ ˜˜^˜˜
./ebwt.h:2243:15: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countFwSideEx' requested here
        if(ltop._fw) countFwSideEx(ltop, tops); // Forward side
                     ^
./ebwt_search_backtrack.h:552:10: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::mapLFEx' requested here
                                ebwt.mapLFEx(ltop, lbot, &pairs[d*8], &pairs[(d*8)+4]);
                                     ^
In file included from ebwt_search.cpp:14:
./ebwt.h:2094:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                if((l._sideByteOff + l._by > _zEbwtByteOff) ||
                                   ˜ ˜˜^˜˜
./ebwt.h:2095:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                   (l._sideByteOff + l._by == _zEbwtByteOff && l._bp > _zEbwtBpOff))
                                   ˜ ˜˜^˜˜
./ebwt.h:2190:59: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
        if(l._sideByteOff <= _zEbwtByteOff && l._sideByteOff + l._by >= _zEbwtByteOff) {
                                                             ˜ ˜˜^˜˜
./ebwt.h:2244:15: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countBwSideEx' requested here
        else         countBwSideEx(ltop, tops); // Backward side
                     ^
./ebwt_search_backtrack.h:552:10: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::mapLFEx' requested here
                                ebwt.mapLFEx(ltop, lbot, &pairs[d*8], &pairs[(d*8)+4]);
                                     ^
In file included from ebwt_search.cpp:14:
./ebwt.h:2193:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                if((l._sideByteOff + l._by > _zEbwtByteOff) ||
                                   ˜ ˜˜^˜˜
./ebwt.h:2194:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                   (l._sideByteOff + l._by == _zEbwtByteOff && l._bp >= _zEbwtBpOff))
                                   ˜ ˜˜^˜˜
./ebwt.h:2035:69: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
        if(c == 0 && l._sideByteOff <= _zEbwtByteOff && l._sideByteOff + l._by >= _zEbwtByteOff) {
                                                                       ˜ ˜˜^˜˜
./ebwt.h:2374:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countFwSide' requested here
        if(l._fw) ret = countFwSide(l, c); // Forward side
                        ^
./ebwt_search_backtrack.h:565:24: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::mapLF1' requested here
                                                bot = top = ebwt.mapLF1(top, ltop, c);
                                                                 ^
In file included from ebwt_search.cpp:14:
./ebwt.h:2038:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                if((l._sideByteOff + l._by > _zEbwtByteOff) ||
                                   ˜ ˜˜^˜˜
./ebwt.h:2039:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                   (l._sideByteOff + l._by == _zEbwtByteOff && l._bp > _zEbwtBpOff))
                                   ˜ ˜˜^˜˜
./ebwt.h:1945:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                cCnt += countInU64(c, *(uint64_t*)&side[i]);
                     ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:2033:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countUpTo' requested here
        uint32_t cCnt = countUpTo(l, c);
                        ^
./ebwt.h:2374:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countFwSide' requested here
        if(l._fw) ret = countFwSide(l, c); // Forward side
                        ^
./ebwt_search_backtrack.h:565:24: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::mapLF1' requested here
                                                bot = top = ebwt.mapLF1(top, ltop, c);
                                                                 ^
In file included from ebwt_search.cpp:14:
./ebwt.h:2140:69: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
        if(c == 0 && l._sideByteOff <= _zEbwtByteOff && l._sideByteOff + l._by >= _zEbwtByteOff) {
                                                                       ˜ ˜˜^˜˜
./ebwt.h:2375:18: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::countBwSide' requested here
        else      ret = countBwSide(l, c); // Backward side
                        ^
./ebwt_search_backtrack.h:565:24: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::mapLF1' requested here
                                                bot = top = ebwt.mapLF1(top, ltop, c);
                                                                 ^
In file included from ebwt_search.cpp:14:
./ebwt.h:2143:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                if((l._sideByteOff + l._by > _zEbwtByteOff) ||
                                   ˜ ˜˜^˜˜
./ebwt.h:2144:26: warning: implicit conversion changes signedness: 'const int16_t' (aka 'const short') to 'unsigned int' [-Wsign-conversion]
                   (l._sideByteOff + l._by == _zEbwtByteOff && l._bp >= _zEbwtBpOff))
                                   ˜ ˜˜^˜˜
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1377:25: note: in instantiation of function template specialization 'seqan::length<QueryMutation, seqan::Alloc<void> >' requested here
                for(size_t i = 0; i < length(*_muts); i++) {
                                      ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:323:17: warning: implicit conversion loses integer precision: 'const int' to 'unsigned char' [-Wconversion]
        target.value = source;
                     ˜ ^˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:82:3: note: in instantiation of function template specialization 'seqan::assign<unsigned char, seqan::_Dna5, int>' requested here
                assign(*this, other);
                ^
./ebwt_search_backtrack.h:1384:21: note: in instantiation of function template specialization 'seqan::SimpleType<unsigned char, seqan::_Dna5>::SimpleType<int>' requested here
                        (*_qry)[m.pos] = (Dna5)(int)m.newBase; // apply it
                                         ^
In file included from ebwt_search.cpp:14:
./ebwt.h:2597:37: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
        const uint32_t offRate = this->_eh._offRate;
                       ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:1550:14: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reportChaseOne' requested here
                        if(_ebwt->reportChaseOne((*_qry), _qual, _name,
                                  ^
In file included from ebwt_search.cpp:14:
./ebwt.h:1285:17: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                hit.stratum = stratum;
                            ˜ ^˜˜˜˜˜˜
./ebwt.h:2528:16: note: in instantiation of member function 'EbwtSearchParams<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reportHit' requested here
        return params.reportHit(
                      ^
./ebwt.h:2634:9: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::report' requested here
        return report(query, quals, name, color, primer, trimc, colExEnds,
               ^
./ebwt_search_backtrack.h:1550:14: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reportChaseOne' requested here
                        if(_ebwt->reportChaseOne((*_qry), _qual, _name,
                                  ^
In file included from ebwt_search.cpp:14:
./ebwt.h:1307:24: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.crefcs[off] = refcs[i];
                                                        ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1310:22: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.crefcs[i] = refcs[i];
                                                      ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1331:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        read[i] = (int)hit.patSeq[i];
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1332:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                        qual[i] = mmPenalty(maqRound, phredCharToPhredQual(hit.quals[i]));
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1340:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                rf[i] = (1 << rf[i]);
                                      ˜  ˜˜^˜˜˜˜˜˜˜
./ebwt.h:1356:39: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        size_t nqlen = qlen + (colExEnds ? -1 : 1);
                                            ˜              ^˜
./ebwt.h:1427:23: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.refcs[off] = refcs[i];
                                                       ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1430:29: warning: implicit conversion changes signedness: 'const unsigned char' to 'char' [-Wsign-conversion]
                                        hit.refcs[mmui32[i]] = refcs[i];
                                                             ˜ ^˜˜˜˜˜˜˜
./ebwt.h:1397:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        uint32_t off = i - (colExEnds? 1:0);
                                                 ˜˜˜   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:1398:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        if(!_fw) off = nqlen - off - 1;
                                                     ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./ebwt.h:1401:60: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        hit.refcs[off] = "ACGT"[ref->getBase(h.first, h.second+i)];
                                                                ˜˜˜                   ˜˜˜˜˜˜˜˜^˜
./ebwt.h:1447:22: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        uint32_t qoff = i;
                                                 ˜˜˜˜   ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:31:
In file included from ./hit.h:15:
./bitset.h:386:17: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        oss << (test(i)? "1" : "0");
                                ˜˜˜˜ ^
./ebwt.h:1459:36: note: in instantiation of member function 'FixedBitset<1024>::str' requested here
                                cerr << "Expected " << hit.mms.str() << " mismatches, got " << diffs.str() << endl;
                                                               ^
./ebwt.h:2528:16: note: in instantiation of member function 'EbwtSearchParams<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reportHit' requested here
        return params.reportHit(
                      ^
./ebwt.h:2634:9: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::report' requested here
        return report(query, quals, name, color, primer, trimc, colExEnds,
               ^
./ebwt_search_backtrack.h:1550:14: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::reportChaseOne' requested here
                        if(_ebwt->reportChaseOne((*_qry), _qual, _name,
                                  ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:1607:
In file included from ./ebwt_search_backtrack.h:10:
./range_source.h:1699:54: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                foundRange(false), done(_done), minCostAdjustment_(minCostAdjustment)
                                                                  ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt_search_backtrack.h:3010:4: note: in instantiation of member function 'RangeSourceDriver<EbwtRangeSource>::RangeSourceDriver' requested here
                        RangeSourceDriver<EbwtRangeSource>(true, 0),
                        ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:1607:
In file included from ./ebwt_search_backtrack.h:10:
./range_source.h:2467:29: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                                vec.erase(vec.begin() + i);
                                          ˜˜˜           ^
./range_source.h:2200:3: note: in instantiation of member function 'CostAwareRangeSourceDriver<EbwtRangeSource>::sortActives' requested here
                sortActives();
                ^
./ebwt_search_backtrack.h:3127:13: note: in instantiation of member function 'CostAwareRangeSourceDriver<EbwtRangeSource>::addSource' requested here
                                rsFull_.addSource(partial, seedRange_);
                                        ^
In file included from ebwt_search.cpp:14:
./ebwt.h:2968:45: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                mmFile[i] = (char*)mmap((void *)0, sbuf.st_size,
                                                   ˜˜˜˜            ˜˜˜˜˜^˜˜˜˜˜˜
./ebwt.h:874:3: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::readIntoMemory' requested here
                readIntoMemory(
                ^
ebwt_search.cpp:1306:8: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::loadIntoMemory' requested here
                ebwt.loadIntoMemory(color ? 1 : 0, -1, !noRefNames, startVerbose);
                     ^
In file included from ebwt_search.cpp:14:
./ebwt.h:3035:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  lineRate     = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜˜       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3037:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  linesPerSide = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3039:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  offRate      = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3045:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t  ftabChars    = readI32(_in1, switchEndian);
                 ˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3049:18: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t flags = readI32(_in1, switchEndian);
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ebwt.h:3096:34: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                offRateDiff = _overrideOffRate - offRate;
                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./ebwt.h:3110:34: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                isaRateDiff = _overrideIsaRate - isaRate;
                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
ebwt_search.cpp:2483:52: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patsrc = new PairedSoloPatternSource(patsrcs_ab, seed);
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜             ^˜˜˜
ebwt_search.cpp:2864:4: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                        driver<String<Dna, Alloc<> > >("DNA", ebwtFile, query, queries, qualities, outfile);
                        ^
ebwt_search.cpp:2485:62: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patsrc = new PairedDualPatternSource(patsrcs_a, patsrcs_b, seed);
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                       ^˜˜˜
ebwt_search.cpp:2577:27: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                                os.erase(os.begin() + i);
                                         ˜˜           ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:1459:57: warning: implicit conversion changes signedness: 'long long' to 'typename Size<String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                  ^˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, long long, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./sequence_io.h:56:5: note: in instantiation of function template specialization 'seqan::resize<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, long long>' requested here
                                resize(ss.back(), baseCutoff);
                                ^
./sequence_io.h:100:3: note: in instantiation of function template specialization 'readSequenceFile<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, const seqan::Tag<seqan::TagFasta_> >' requested here
                readSequenceFile<TStr,TFile>(infiles[i], ss, baseCutoff, seqCutoff, reverse);
                ^
./sequence_io.h:116:2: note: in instantiation of function template specialization 'readSequenceFiles<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, const seqan::Tag<seqan::TagFasta_> >' requested here
        readSequenceFiles<TStr,TFile>(infiles, ss, i, seqCutoff, reverse);
        ^
ebwt_search.cpp:2368:4: note: in instantiation of function template specialization 'readSequenceFiles<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, const seqan::Tag<seqan::TagFasta_> >' requested here
                        readSequenceFiles<String<Dna5>, Fasta>(origFiles, os);
                        ^
ebwt_search.cpp:2864:4: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                        driver<String<Dna, Alloc<> > >("DNA", ebwtFile, query, queries, qualities, outfile);
                        ^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
In file included from ./diff_sample.h:8:
In file included from ./multikey_qsort.h:8:
./sequence_io.h:138:26: warning: implicit conversion changes signedness: 'int64_t' (aka 'long long') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        stmp = stmp.substr(0, baseCutoff);
                               ˜˜˜˜           ^˜˜˜˜˜˜˜˜˜
./sequence_io.h:171:2: note: in instantiation of function template specialization 'readSequenceString<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >' requested here
        readSequenceString(s, ss, i, seqCutoff, reverse);
        ^
ebwt_search.cpp:2371:4: note: in instantiation of function template specialization 'readSequenceString<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >' requested here
                        readSequenceString(origString, os);
                        ^
ebwt_search.cpp:2864:4: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                        driver<String<Dna, Alloc<> > >("DNA", ebwtFile, query, queries, qualities, outfile);
                        ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:1421:21: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >' requested here
                TSize me_length = length(me);
                                  ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
./ebwt.h:2817:2: note: in instantiation of function template specialization 'seqan::resize<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        resize(s, this->_eh._len, Exact());
        ^
./ebwt.h:2844:2: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::restore' requested here
        restore(rest);
        ^
ebwt_search.cpp:2590:8: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::checkOrigs' requested here
                ebwt.checkOrigs(os, color, false);
                     ^
ebwt_search.cpp:2864:4: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                        driver<String<Dna, Alloc<> > >("DNA", ebwtFile, query, queries, qualities, outfile);
                        ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<seqan::SimpleType<unsigned char, seqan::_Dna> >' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<seqan::SimpleType<unsigned char, seqan::_Dna>, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
./ebwt.h:2817:2: note: in instantiation of function template specialization 'seqan::resize<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        resize(s, this->_eh._len, Exact());
        ^
./ebwt.h:2844:2: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::restore' requested here
        restore(rest);
        ^
ebwt_search.cpp:2590:8: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::checkOrigs' requested here
                ebwt.checkOrigs(os, color, false);
                     ^
ebwt_search.cpp:2864:4: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                        driver<String<Dna, Alloc<> > >("DNA", ebwtFile, query, queries, qualities, outfile);
                        ^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:323:17: warning: implicit conversion loses integer precision: 'const int' to 'unsigned char' [-Wconversion]
        target.value = source;
                     ˜ ^˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:98:3: note: in instantiation of function template specialization 'seqan::assign<unsigned char, seqan::_Dna, int>' requested here
                assign(*this, other);
                ^
./ebwt.h:2827:33: note: in instantiation of function template specialization 'seqan::SimpleType<unsigned char, seqan::_Dna>::operator=<int>' requested here
                s[this->_eh._len - jumps - 1] = rowL(l);
                                              ^
./ebwt.h:2844:2: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::restore' requested here
        restore(rest);
        ^
ebwt_search.cpp:2590:8: note: in instantiation of member function 'Ebwt<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >::checkOrigs' requested here
                ebwt.checkOrigs(os, color, false);
                     ^
ebwt_search.cpp:2864:4: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                        driver<String<Dna, Alloc<> > >("DNA", ebwtFile, query, queries, qualities, outfile);
                        ^
ebwt_search.cpp:2242:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<tthread::thread*> threads(nthreads);
                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:2680:4: note: in instantiation of function template specialization 'seededQualCutoffSearchFull<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                        seededQualCutoffSearchFull(seedLen,
                        ^
ebwt_search.cpp:2864:4: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                        driver<String<Dna, Alloc<> > >("DNA", ebwtFile, query, queries, qualities, outfile);
                        ^
ebwt_search.cpp:2243:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<int> tids(nthreads);
                       ˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:2258:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        tids[i] = i+1;
                        ˜˜˜˜ ^
ebwt_search.cpp:2260:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(seededQualSearchWorkerFullStateful, (void*)&tids[i]);
                                ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:2260:115: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(seededQualSearchWorkerFullStateful, (void*)&tids[i]);
                                                                                                             ˜˜˜˜ ^
ebwt_search.cpp:2262:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(seededQualSearchWorkerFull, (void*)&tids[i]);
                                ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:2262:107: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                threads[i] = new tthread::thread(seededQualSearchWorkerFull, (void*)&tids[i]);
                                                                                                     ˜˜˜˜ ^
ebwt_search.cpp:2266:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                    threads[i]->join();
                    ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1864:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<tthread::thread*> threads(nthreads);
                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:2694:5: note: in instantiation of function template specialization 'twoOrThreeMismatchSearchFull<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                                twoOrThreeMismatchSearchFull(*patsrc, *sink, ebwt, *ebwtBw, os, mismatches == 2);
                                ^
ebwt_search.cpp:2864:4: note: in instantiation of function template specialization 'driver<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> > >' requested here
                        driver<String<Dna, Alloc<> > >("DNA", ebwtFile, query, queries, qualities, outfile);
                        ^
ebwt_search.cpp:1865:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        AutoArray<int> tids(nthreads);
                       ˜˜˜˜ ^˜˜˜˜˜˜˜
ebwt_search.cpp:1871:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        tids[i] = i+1;
                        ˜˜˜˜ ^
ebwt_search.cpp:1873:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                            threads[i] = new tthread::thread(twoOrThreeMismatchSearchWorkerStateful, (void*)&tids[i]);
                            ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1873:115: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                            threads[i] = new tthread::thread(twoOrThreeMismatchSearchWorkerStateful, (void*)&tids[i]);
                                                                                                             ˜˜˜˜ ^
ebwt_search.cpp:1875:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                            threads[i] = new tthread::thread(twoOrThreeMismatchSearchWorkerFull, (void *)&tids[i]);
                            ˜˜˜˜˜˜˜ ^
ebwt_search.cpp:1875:112: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                            threads[i] = new tthread::thread(twoOrThreeMismatchSearchWorkerFull, (void *)&tids[i]);
                                                                                                          ˜˜˜˜ ^
ebwt_search.cpp:1879:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                    threads[i]->join();
                    ˜˜˜˜˜˜˜ ^
In file included from ebwt_search.cpp:25:
./aligner.h:442:8: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                                ra.stratum,               // alignment stratum
                                ˜˜˜^˜˜˜˜˜˜
./aligner.h:465:18: note: in instantiation of member function 'UnpairedAlignerV2<EbwtRangeSource>::report' requested here
                                this->done = report(driver_->range(), rchase_->off().first,
                                             ^
./aligner_0mm.h:111:14: note: in instantiation of member function 'UnpairedAlignerV2<EbwtRangeSource>::advance' requested here
                return new UnpairedAlignerV2<EbwtRangeSource>(
                           ^
In file included from ebwt_search.cpp:25:
In file included from ./aligner.h:20:
./ref_aligner.h:306:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./aligner_0mm.h:310:10: note: in instantiation of member function 'ExactRefAligner<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >::anchor64Find' requested here
                        = new ExactRefAligner<String<Dna5> >(color_, verbose_, quiet_);
                              ^
In file included from ebwt_search.cpp:25:
In file included from ./aligner.h:20:
./ref_aligner.h:306:44: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:321:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:346:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor  = ((anchor  << 2llu) | c);
                                                     ˜ ^
./ref_aligner.h:347:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:385:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:296:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t qlen = seqan::length(qry);
                               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search.cpp:25:
./aligner.h:950:16: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                int minins = minInsert_;
                    ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜
./aligner.h:1083:19: note: in instantiation of member function 'PairedBWAlignerV1<EbwtRangeSource>::resolveOutstandingInRef' requested here
                                        this->done = resolveOutstandingInRef(
                                                     ^
./aligner.h:794:3: note: in instantiation of member function 'PairedBWAlignerV1<EbwtRangeSource>::advanceOrientation' requested here
                advanceOrientation(!doneFw_);
                ^
./aligner_0mm.h:317:49: note: in instantiation of member function 'PairedBWAlignerV1<EbwtRangeSource>::advance' requested here
                        PairedBWAlignerV1<EbwtRangeSource>* al = new PairedBWAlignerV1<EbwtRangeSource>(
                                                                     ^
In file included from ebwt_search.cpp:25:
./aligner.h:951:16: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                int maxins = maxInsert_;
                    ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜
./aligner.h:989:29: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                uint32_t insDiff = maxins - minins;
                         ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./aligner.h:991:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        end = toff + maxins;
                                   ˜ ^˜˜˜˜˜
./aligner.h:1010:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                begin = toff + alen - maxins;
                                                    ˜ ^˜˜˜˜˜
./aligner.h:1017:44: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                end = min<uint32_t>(end, toff + alen - minins + qlen - 1);
                                                                     ˜ ^˜˜˜˜˜
./aligner.h:947:19: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t qlen = seqan::length(seq);  // length of outstanding mate
                         ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./aligner.h:853:5: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                lenR,                         // mate length
                                ^˜˜˜
./aligner.h:1045:7: note: in instantiation of member function 'PairedBWAlignerV1<EbwtRangeSource>::report' requested here
                        if(report(
                           ^
./aligner.h:1083:19: note: in instantiation of member function 'PairedBWAlignerV1<EbwtRangeSource>::resolveOutstandingInRef' requested here
                                        this->done = resolveOutstandingInRef(
                                                     ^
./aligner.h:794:3: note: in instantiation of member function 'PairedBWAlignerV1<EbwtRangeSource>::advanceOrientation' requested here
                advanceOrientation(!doneFw_);
                ^
./aligner_0mm.h:317:49: note: in instantiation of member function 'PairedBWAlignerV1<EbwtRangeSource>::advance' requested here
                        PairedBWAlignerV1<EbwtRangeSource>* al = new PairedBWAlignerV1<EbwtRangeSource>(
                                                                     ^
In file included from ebwt_search.cpp:25:
./aligner.h:857:8: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                                rL.stratum,                   // alignment stratum
                                ˜˜˜^˜˜˜˜˜˜
./aligner.h:888:5: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                lenL,                         // mate length
                                ^˜˜˜
./aligner.h:892:8: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                                rR.stratum,                   // alignment stratum
                                ˜˜˜^˜˜˜˜˜˜
./aligner.h:1900:16: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                int minins = minInsert_;
                    ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜
./aligner.h:1837:15: note: in instantiation of member function 'PairedBWAlignerV2<EbwtRangeSource>::resolveOutstandingInRef' requested here
                        bool ret = resolveOutstandingInRef(off, tlen, range);
                                   ^
./aligner.h:1592:5: note: in instantiation of member function 'PairedBWAlignerV2<EbwtRangeSource>::resolveOutstanding' requested here
                                resolveOutstanding(
                                ^
./aligner_0mm.h:335:49: note: in instantiation of member function 'PairedBWAlignerV2<EbwtRangeSource>::advance' requested here
                        PairedBWAlignerV2<EbwtRangeSource>* al = new PairedBWAlignerV2<EbwtRangeSource>(
                                                                     ^
In file included from ebwt_search.cpp:25:
./aligner.h:1901:16: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                int maxins = maxInsert_;
                    ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜
./aligner.h:1930:29: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                uint32_t insDiff = maxins - minins;
                         ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./aligner.h:1932:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        end = toff + maxins;
                                   ˜ ^˜˜˜˜˜
./aligner.h:1951:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                begin = toff + alen - maxins;
                                                    ˜ ^˜˜˜˜˜
./aligner.h:1958:44: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                end = min<uint32_t>(end, toff + alen - minins + qlen - 1);
                                                                     ˜ ^˜˜˜˜˜
./aligner.h:1897:19: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t qlen = seqan::length(seq);  // length of outstanding mate
                         ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./aligner.h:1732:5: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                lenR,                         // mate length
                                ^˜˜˜
./aligner.h:1982:7: note: in instantiation of member function 'PairedBWAlignerV2<EbwtRangeSource>::report' requested here
                        if(report(
                           ^
./aligner.h:1837:15: note: in instantiation of member function 'PairedBWAlignerV2<EbwtRangeSource>::resolveOutstandingInRef' requested here
                        bool ret = resolveOutstandingInRef(off, tlen, range);
                                   ^
./aligner.h:1592:5: note: in instantiation of member function 'PairedBWAlignerV2<EbwtRangeSource>::resolveOutstanding' requested here
                                resolveOutstanding(
                                ^
./aligner_0mm.h:335:49: note: in instantiation of member function 'PairedBWAlignerV2<EbwtRangeSource>::advance' requested here
                        PairedBWAlignerV2<EbwtRangeSource>* al = new PairedBWAlignerV2<EbwtRangeSource>(
                                                                     ^
In file included from ebwt_search.cpp:25:
./aligner.h:1736:8: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                                rL.stratum,                   // alignment stratum
                                ˜˜˜^˜˜˜˜˜˜
./aligner.h:1767:5: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                lenL,                         // mate length
                                ^˜˜˜
./aligner.h:1771:8: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                                rR.stratum,                   // alignment stratum
                                ˜˜˜^˜˜˜˜˜˜
./aligner.h:1818:6: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                        r.stratum,               // alignment stratum
                        ˜˜^˜˜˜˜˜˜
./aligner.h:1853:5: note: in instantiation of member function 'PairedBWAlignerV2<EbwtRangeSource>::reportSe' requested here
                                reportSe(range, off, tlen);
                                ^
./aligner.h:1592:5: note: in instantiation of member function 'PairedBWAlignerV2<EbwtRangeSource>::resolveOutstanding' requested here
                                resolveOutstanding(
                                ^
./aligner_0mm.h:335:49: note: in instantiation of member function 'PairedBWAlignerV2<EbwtRangeSource>::advance' requested here
                        PairedBWAlignerV2<EbwtRangeSource>* al = new PairedBWAlignerV2<EbwtRangeSource>(
                                                                     ^
In file included from ebwt_search.cpp:25:
In file included from ./aligner.h:20:
./ref_aligner.h:650:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./aligner_1mm.h:422:8: note: in instantiation of member function 'OneMMRefAligner<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >::anchor64Find' requested here
                        new OneMMRefAligner<String<Dna5> >(color_, verbose_, quiet_);
                            ^
In file included from ebwt_search.cpp:25:
In file included from ./aligner.h:20:
./ref_aligner.h:650:44: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:651:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:704:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor  = ((anchor  << 2llu) | c);
                                                     ˜ ^
./ref_aligner.h:705:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:748:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:802:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos = nPos;
                                      ˜ ^˜˜˜
./ref_aligner.h:803:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc = "ACGT"[(int)ref[rir + nPos]];
                                                           ˜ ^˜˜˜
./ref_aligner.h:894:27: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                range.refcs.push_back(refc);
                                ˜˜˜˜˜                 ^˜˜˜
./ref_aligner.h:640:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t qlen = seqan::length(qry);
                               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:1069:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./aligner_23mm.h:615:21: note: in instantiation of member function 'TwoMMRefAligner<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >::anchor64Find' requested here
                        refAligner = new TwoMMRefAligner<String<Dna5> >(color_, verbose_, quiet_);
                                         ^
In file included from ebwt_search.cpp:25:
In file included from ./aligner.h:20:
./ref_aligner.h:1069:44: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:1070:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:1130:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor  = ((anchor  << 2llu) | c);
                                                     ˜ ^
./ref_aligner.h:1131:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:1175:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:1232:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos1 = nPos1;
                                       ˜ ^˜˜˜˜
./ref_aligner.h:1233:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc1 = "ACGT"[(int)ref[rir + nPos1]];
                                                            ˜ ^˜˜˜˜
./ref_aligner.h:1235:15: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        mmpos2 = nPos2;
                                               ˜ ^˜˜˜˜
./ref_aligner.h:1236:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        refc2 = "ACGT"[(int)ref[rir + nPos2]];
                                                                    ˜ ^˜˜˜˜
./ref_aligner.h:1364:27: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                range.refcs.push_back(refc1);
                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1371:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc2);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1059:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t qlen = seqan::length(qry);
                               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:1559:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./aligner_23mm.h:617:21: note: in instantiation of member function 'ThreeMMRefAligner<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >::anchor64Find' requested here
                        refAligner = new ThreeMMRefAligner<String<Dna5> >(color_, verbose_, quiet_);
                                         ^
In file included from ebwt_search.cpp:25:
In file included from ./aligner.h:20:
./ref_aligner.h:1559:44: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(qlen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:1560:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:1625:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor  = ((anchor  << 2llu) | c);
                                                     ˜ ^
./ref_aligner.h:1626:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:1670:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:1730:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos1 = nPos1;
                                       ˜ ^˜˜˜˜
./ref_aligner.h:1731:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc1 = "ACGT"[(int)ref[rir + nPos1]];
                                                            ˜ ^˜˜˜˜
./ref_aligner.h:1733:15: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        mmpos2 = nPos2;
                                               ˜ ^˜˜˜˜
./ref_aligner.h:1734:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        refc2 = "ACGT"[(int)ref[rir + nPos2]];
                                                                    ˜ ^˜˜˜˜
./ref_aligner.h:1736:16: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                mmpos3 = nPos3;
                                                       ˜ ^˜˜˜˜
./ref_aligner.h:1737:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                refc3 = "ACGT"[(int)ref[rir + nPos3]];
                                                                            ˜ ^˜˜˜˜
./ref_aligner.h:1909:27: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                range.refcs.push_back(refc1);
                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1916:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc2);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1923:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc3);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:1549:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t qlen = seqan::length(qry);
                               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:2191:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:670:21: note: in instantiation of member function 'Seed0RefAligner<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >::anchor64Find' requested here
                        refAligner = new Seed0RefAligner<String<Dna5> >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_);
                                         ^
In file included from ebwt_search.cpp:25:
In file included from ./aligner.h:20:
./ref_aligner.h:2191:44: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:2192:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:2269:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor = ((anchor << 2llu) | c);
                                                   ˜ ^
./ref_aligner.h:2270:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:2325:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:2449:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:2450:43: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                ham += mmPenalty(this->maqPenalty_, q);
                                                       ˜˜˜˜˜˜˜˜˜                    ^
./ref_aligner.h:2460:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[rc]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:2511:19: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        range.numMms = mms;
                                     ˜ ^˜˜
./ref_aligner.h:2179:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t qlen = seqan::length(qry);
                               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:2816:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:672:21: note: in instantiation of member function 'Seed1RefAligner<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >::anchor64Find' requested here
                        refAligner = new Seed1RefAligner<String<Dna5> >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_);
                                         ^
In file included from ebwt_search.cpp:25:
In file included from ./aligner.h:20:
./ref_aligner.h:2816:44: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:2817:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:2907:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor = ((anchor << 2llu) | c);
                                                   ˜ ^
./ref_aligner.h:2908:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:2965:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:3020:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos = nPos;
                                      ˜ ^˜˜˜
./ref_aligner.h:3022:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc = "ACGT"[(int)ref[rir + nPos]];
                                                           ˜ ^˜˜˜
./ref_aligner.h:3107:17: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                        char q = phredCharToPhredQual(quals[qoff]);
                                                             ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:3108:44: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                        ham += mmPenalty(this->maqPenalty_, q);
                                                               ˜˜˜˜˜˜˜˜˜                    ^
./ref_aligner.h:3125:14: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        int mms = diffs; // start counting total mismatches
                            ˜˜˜   ^˜˜˜˜
./ref_aligner.h:3164:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:3165:43: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                ham += mmPenalty(this->maqPenalty_, q);
                                                       ˜˜˜˜˜˜˜˜˜                    ^
./ref_aligner.h:3175:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[rc]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:3228:19: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        range.numMms = mms;
                                     ˜ ^˜˜
./ref_aligner.h:3242:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc);
                                        ˜˜˜˜˜                 ^˜˜˜
./ref_aligner.h:3263:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc);
                                        ˜˜˜˜˜                 ^˜˜˜
./ref_aligner.h:2804:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t qlen = seqan::length(qry);
                               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:3573:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:674:21: note: in instantiation of member function 'Seed2RefAligner<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >::anchor64Find' requested here
                        refAligner = new Seed2RefAligner<String<Dna5> >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_);
                                         ^
In file included from ebwt_search.cpp:25:
In file included from ./aligner.h:20:
./ref_aligner.h:3573:44: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:3574:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:3675:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor = ((anchor << 2llu) | c);
                                                   ˜ ^
./ref_aligner.h:3676:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:3733:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:3794:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos1 = nPos1;
                                       ˜ ^˜˜˜˜
./ref_aligner.h:3795:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc1 = "ACGT"[(int)ref[rir + nPos1]];
                                                            ˜ ^˜˜˜˜
./ref_aligner.h:3806:15: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        mmpos2 = nPos2;
                                               ˜ ^˜˜˜˜
./ref_aligner.h:3807:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        refc2 = "ACGT"[(int)ref[rir + nPos2]];
                                                                    ˜ ^˜˜˜˜
./ref_aligner.h:3944:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:3945:43: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                ham += mmPenalty(this->maqPenalty_, q);
                                                       ˜˜˜˜˜˜˜˜˜                    ^
./ref_aligner.h:3961:14: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        int mms = diffs; // start counting total mismatches
                            ˜˜˜   ^˜˜˜˜
./ref_aligner.h:4000:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:4001:43: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                ham += mmPenalty(this->maqPenalty_, q);
                                                       ˜˜˜˜˜˜˜˜˜                    ^
./ref_aligner.h:4011:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[rc]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:4064:19: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        range.numMms = mms;
                                     ˜ ^˜˜
./ref_aligner.h:4078:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc1);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4089:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc2);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4111:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc1);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4122:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc2);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:3561:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t qlen = seqan::length(qry);
                               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:4453:35: warning: implicit conversion changes signedness: 'const int' to 'const uint32_t' (aka 'const unsigned int') [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./aligner_seed_mm.h:676:21: note: in instantiation of member function 'Seed3RefAligner<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >::anchor64Find' requested here
                        refAligner = new Seed3RefAligner<String<Dna5> >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_);
                                         ^
In file included from ebwt_search.cpp:25:
In file included from ./aligner.h:20:
./ref_aligner.h:4453:44: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                const uint32_t anchorBitPairs = min<int>(slen, 32);
                                                ˜˜˜      ^˜˜˜
./ref_aligner.h:4454:46: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                const int lhsShift = ((anchorBitPairs - 1) << 1);
                          ˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ref_aligner.h:4559:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        anchor = ((anchor << 2llu) | c);
                                                   ˜ ^
./ref_aligner.h:4560:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                        buffw = ((buffw << 2llu) | r);
                                                 ˜ ^
./ref_aligner.h:4617:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                                buffw = ((buffw << 2llu) | r);
                                                         ˜ ^
./ref_aligner.h:4682:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                mmpos1 = nPos1;
                                       ˜ ^˜˜˜˜
./ref_aligner.h:4683:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                refc1 = "ACGT"[(int)ref[rir + nPos1]];
                                                            ˜ ^˜˜˜˜
./ref_aligner.h:4694:15: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        mmpos2 = nPos2;
                                               ˜ ^˜˜˜˜
./ref_aligner.h:4695:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        refc2 = "ACGT"[(int)ref[rir + nPos2]];
                                                                    ˜ ^˜˜˜˜
./ref_aligner.h:4706:16: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                mmpos3 = nPos3;
                                                       ˜ ^˜˜˜˜
./ref_aligner.h:4707:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                refc3 = "ACGT"[(int)ref[rir + nPos3]];
                                                                            ˜ ^˜˜˜˜
./ref_aligner.h:4902:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:4903:43: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                ham += mmPenalty(this->maqPenalty_, q);
                                                       ˜˜˜˜˜˜˜˜˜                    ^
./ref_aligner.h:4919:14: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        int mms = diffs; // start counting total mismatches
                            ˜˜˜   ^˜˜˜˜
./ref_aligner.h:4958:16: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                                                char q = phredCharToPhredQual(quals[qoff]);
                                                     ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:4959:43: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                                                ham += mmPenalty(this->maqPenalty_, q);
                                                       ˜˜˜˜˜˜˜˜˜                    ^
./ref_aligner.h:4969:30: warning: implicit conversion changes signedness: 'const char' to 'const value_type' (aka 'const unsigned char') [-Wsign-conversion]
                                                nonSeedRefcs.push_back("ACGTN"[rc]);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜
./ref_aligner.h:5022:19: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        range.numMms = mms;
                                     ˜ ^˜˜
./ref_aligner.h:5036:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc1);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:5046:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc2);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:5057:30: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                        range.refcs.push_back(refc3);
                                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:5080:28: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                        range.refcs.push_back(refc1);
                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:5090:29: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                range.refcs.push_back(refc2);
                                                ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:5101:30: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const unsigned char') [-Wconversion]
                                                        range.refcs.push_back(refc3);
                                                        ˜˜˜˜˜                 ^˜˜˜˜
./ref_aligner.h:4441:25: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'const uint32_t' (aka 'const unsigned int') [-Wshorten-64-to-32]
                const uint32_t qlen = seqan::length(qry);
                               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
In file included from ./blockwise_sa.h:13:
./diff_sample.h:49:27: warning: variable 'clDCs' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static struct sampleEntry clDCs[16];
                          ^
./diff_sample.h:50:13: warning: variable 'clDCs_calced' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static bool clDCs_calced = false; /// have clDCs been calculated?
            ^
./diff_sample.h:320:17: warning: variable 'dc0to64' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static uint32_t dc0to64[65][10] = {
                ^
In file included from ebwt_search.cpp:22:
./range_cache.h:340:11: warning: private field 'sanity_' is not used [-Wunused-private-field]
        bool     sanity_;  /// do consistency checks?
                 ^
In file included from ebwt_search.cpp:26:
./aligner_0mm.h:119:22: warning: private field 'ebwtBw_' is not used [-Wunused-private-field]
        Ebwt<String<Dna> >* ebwtBw_;
                            ^
./aligner_0mm.h:136:11: warning: private field 'seed_' is not used [-Wunused-private-field]
        uint32_t seed_;
                 ^
./aligner_0mm.h:351:22: warning: private field 'ebwtBw_' is not used [-Wunused-private-field]
        Ebwt<String<Dna> >* ebwtBw_;
                            ^
./aligner_0mm.h:379:17: warning: private field 'seed_' is not used [-Wunused-private-field]
        const uint32_t seed_;
                       ^
In file included from ebwt_search.cpp:27:
./aligner_1mm.h:173:11: warning: private field 'seed_' is not used [-Wunused-private-field]
        uint32_t seed_;
                 ^
./aligner_1mm.h:491:17: warning: private field 'seed_' is not used [-Wunused-private-field]
        const uint32_t seed_;
                       ^
In file included from ebwt_search.cpp:28:
./aligner_23mm.h:243:11: warning: private field 'seed_' is not used [-Wunused-private-field]
        uint32_t seed_;
                 ^
./aligner_23mm.h:688:17: warning: private field 'seed_' is not used [-Wunused-private-field]
        const uint32_t seed_;
                       ^
1220 warnings generated.
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:52:
SeqAn-1.1/seqan/basic/basic_profile.h:161:14: warning: implicit conversion changes signedness: '_proInt' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
        return (_proData<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:54:
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:70:22: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
        const int DEFAULT = ˜(˜0u >> 1); // initialize with the smallest int
                  ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:229:116: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
                finline static void run(unsigned char* ptr, unsigned char c) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
                                                                                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1131:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1140:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char)c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1149:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1167:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1178:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna5<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1187:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1196:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1205:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna5<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1226:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Iupac<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1235:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1244:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1251:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1258:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1269:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_AA<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1278:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1287:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:46:
SeqAn-1.1/seqan/file/cstream.h:142:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return getc(source);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:170:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:181:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:193:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
SeqAn-1.1/seqan/file/cstream.h:205:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:12:
In file included from ./alphabet.h:9:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:14:
./filebuf.h:73:61: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(_lastn_cur < LASTN_BUF_SZ) _lastn_buf[_lastn_cur++] = c;
                                                                               ˜ ^
./filebuf.h:158:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _inf->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:161:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _ins->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:478:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = slen;
                                     ˜ ^˜˜˜
./filebuf.h:505:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = len;
                                     ˜ ^˜˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:15:
In file included from ./word_io.h:8:
./endian_swap.h:23:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        tmp |= ((u << 24) & (0xff << 24));
                          ˜  ˜˜˜˜˜^˜˜˜˜
./endian_swap.h:32:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 56) & (0xffull <<  0));
                             ^
./endian_swap.h:33:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 40) & (0xffull <<  8));
                             ^
./endian_swap.h:34:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >> 24) & (0xffull << 16));
                             ^
./endian_swap.h:35:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u >>  8) & (0xffull << 24));
                             ^
./endian_swap.h:36:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u <<  8) & (0xffull << 32));
                             ^
./endian_swap.h:37:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 24) & (0xffull << 40));
                             ^
./endian_swap.h:38:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 40) & (0xffull << 48));
                             ^
./endian_swap.h:39:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        tmp |= ((u << 56) & (0xffull << 56));
                             ^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:15:
./word_io.h:119:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return endianSwapI32(x);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./word_io.h:121:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return x;
                ˜˜˜˜˜˜ ^
./word_io.h:135:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return endianSwapI32(x);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./word_io.h:137:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                return x;
                ˜˜˜˜˜˜ ^
In file included from ref_read.cpp:1:
./ref_read.h:173:31: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                if (name) name->push_back(c);
                                          ˜˜˜˜            ^
ref_read.cpp:61:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, len, first);
                               ˜˜˜˜˜˜˜˜˜ ^˜˜
ref_read.cpp:61:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, len, first);
                               ˜˜˜˜˜˜˜˜˜      ^˜˜
ref_read.cpp:98:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, 0, first);
                               ˜˜˜˜˜˜˜˜˜ ^˜˜
ref_read.cpp:109:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, 0, first);
                               ˜˜˜˜˜˜˜˜˜ ^˜˜
ref_read.cpp:148:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, len, first);
                               ˜˜˜˜˜˜˜˜˜ ^˜˜
ref_read.cpp:148:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        return RefRecord(off, len, first);
                               ˜˜˜˜˜˜˜˜˜      ^˜˜
ref_read.cpp:165:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return RefRecord(off, len, first);
               ˜˜˜˜˜˜˜˜˜ ^˜˜
ref_read.cpp:165:24: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return RefRecord(off, len, first);
               ˜˜˜˜˜˜˜˜˜      ^˜˜
ref_read.cpp:188:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        bool first = (i == (int)src.size()-1 || src[i+1].first);
                                                                ˜˜˜ ˜^˜
ref_read.cpp:189:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if(src[i].len) {
                           ˜˜˜ ^
ref_read.cpp:190:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                cur.push_back(RefRecord(0, src[i].len, first));
                                                           ˜˜˜ ^
ref_read.cpp:193:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if(src[i].off) cur.push_back(RefRecord(src[i].off, 0, first));
                           ˜˜˜ ^
ref_read.cpp:193:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if(src[i].off) cur.push_back(RefRecord(src[i].off, 0, first));
                                                               ˜˜˜ ^
ref_read.cpp:197:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if(i < (int)cur.size()-1 && cur[i].off != 0 && !cur[i+1].first) {
                                                    ˜˜˜ ^
ref_read.cpp:197:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if(i < (int)cur.size()-1 && cur[i].off != 0 && !cur[i+1].first) {
                                                                        ˜˜˜ ˜^˜
ref_read.cpp:198:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                dst.push_back(RefRecord(cur[i].off, cur[i+1].len, cur[i].first));
                                                        ˜˜˜ ^
ref_read.cpp:198:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                dst.push_back(RefRecord(cur[i].off, cur[i+1].len, cur[i].first));
                                                                    ˜˜˜ ˜^˜
ref_read.cpp:198:59: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                dst.push_back(RefRecord(cur[i].off, cur[i+1].len, cur[i].first));
                                                                                  ˜˜˜ ^
ref_read.cpp:201:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                dst.push_back(cur[i]);
                                              ˜˜˜ ^
ref_read.cpp:187:25: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                for(int i = src.size()-1; i >= 0; i--) {
                        ˜   ˜˜˜˜˜˜˜˜˜˜^˜
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:77:16: note: in instantiation of function template specialization 'seqan::length<char, seqan::Alloc<void> >' requested here
        size_t plen = length(path);
                      ^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./alphabet.h:144:19: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >' requested here
        size_t readLen = seqan::length(read);
                         ^
66 warnings generated.
In file included from edit.cpp:9:
In file included from ./edit.h:13:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from edit.cpp:9:
In file included from ./edit.h:14:
./filebuf.h:73:61: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(_lastn_cur < LASTN_BUF_SZ) _lastn_buf[_lastn_cur++] = c;
                                                                               ˜ ^
./filebuf.h:158:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _inf->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:161:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _ins->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:478:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = slen;
                                     ˜ ^˜˜˜
./filebuf.h:505:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = len;
                                     ˜ ^˜˜
In file included from edit.cpp:9:
./edit.h:36:7: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                   ˜^˜
./edit.h:36:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                      ˜^˜
./edit.h:36:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                               ˜^˜
9 warnings generated.
In file included from tinythread.cpp:25:
./tinythread.h:631:9: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
typedef long long __intmax_t;
        ^
tinythread.cpp:279:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  return (int) sysconf(_SC_NPROCESSORS_ONLN);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:52:
SeqAn-1.1/seqan/basic/basic_profile.h:161:14: warning: implicit conversion changes signedness: '_proInt' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
        return (_proData<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:54:
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:70:22: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
        const int DEFAULT = ˜(˜0u >> 1); // initialize with the smallest int
                  ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:229:116: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
                finline static void run(unsigned char* ptr, unsigned char c) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
                                                                                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1131:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1140:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char)c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1149:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1167:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1178:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna5<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1187:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1196:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1205:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna5<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1226:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Iupac<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1235:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1244:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1251:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1258:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1269:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_AA<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1278:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1287:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from pat.cpp:6:
In file included from SeqAn-1.1/seqan/file.h:46:
SeqAn-1.1/seqan/file/cstream.h:142:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return getc(source);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:170:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:181:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:193:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
SeqAn-1.1/seqan/file/cstream.h:205:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
In file included from pat.cpp:8:
In file included from ./pat.h:13:
In file included from ./alphabet.h:9:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from pat.cpp:8:
In file included from ./pat.h:17:
In file included from ./threading.h:5:
./tinythread.h:631:9: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
typedef long long __intmax_t;
        ^
In file included from pat.cpp:8:
In file included from ./pat.h:18:
./filebuf.h:73:61: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(_lastn_cur < LASTN_BUF_SZ) _lastn_buf[_lastn_cur++] = c;
                                                                               ˜ ^
./filebuf.h:158:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _inf->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:161:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _ins->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:478:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = slen;
                                     ˜ ^˜˜˜
./filebuf.h:505:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = len;
                                     ˜ ^˜˜
In file included from pat.cpp:8:
In file included from ./pat.h:19:
./qual.h:93:40: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
                char cc = solexaToPhred((int)c - 64) + 33;
                     ˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./qual.h:147:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return (int)pQ;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜
./qual.h:161:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:165:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./qual.h:188:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:191:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from pat.cpp:8:
In file included from ./pat.h:20:
In file included from ./hit_set.h:16:
./edit.h:36:7: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                   ˜^˜
./edit.h:36:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                      ˜^˜
./edit.h:36:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                               ˜^˜
In file included from pat.cpp:8:
In file included from ./pat.h:20:
./hit_set.h:37:12: warning: implicit conversion changes signedness: 'const uint8_t' (aka 'const unsigned char') to 'char' [-Wsign-conversion]
                fb.write(fw);
                ˜˜       ^˜
./hit_set.h:44:17: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t sz = edits.size();
                         ˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:50:8: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                sz = cedits.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:63:8: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                fw = fb.get();
                   ˜ ^˜˜˜˜˜˜˜
./hit_set.h:65:13: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                stratum = fb.get();
                        ˜ ^˜˜˜˜˜˜˜
./hit_set.h:244:16: warning: implicit conversion loses integer precision: 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t i = seqan::length(name);
                         ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:248:7: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = seqan::length(seq);
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:256:7: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = ents.size();
                  ˜ ^˜˜˜˜˜˜˜˜˜˜
./hit_set.h:298:18: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                maxedStratum = fb.get();
                             ˜ ^˜˜˜˜˜˜˜
./hit_set.h:391:29: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                ents.erase(ents.begin() + i);
                           ˜˜˜˜           ^
In file included from pat.cpp:8:
./pat.h:53:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:61:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:70:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:167:10: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                return seqan::length(patFw);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:723:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t ret = 0llu;
                               ^
./pat.h:728:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                return make_pair(ret, 0llu);
                                      ^
./pat.h:875:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                ^
./pat.h:875:32: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                             ^
./pat.h:1087:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1105:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1126:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, length);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1128:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, length);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:1129:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                itoa10(patid, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜
./pat.h:1164:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1169:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1183:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                patid_ += numthreads_;
                       ˜˜ ^˜˜˜˜˜˜˜˜˜˜
./pat.h:1188:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1189:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1358:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        s.erase(0, mytrim5);
                                        ˜          ^˜˜˜˜˜˜
./pat.h:1362:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        s.erase(s.length()-trim3_);
                                                          ˜^˜˜˜˜˜
./pat.h:1374:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        vq.erase(0, mytrim5);
                                        ˜˜          ^˜˜˜˜˜˜
./pat.h:1378:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        vq.erase(vq.length()-trim3_);
                                                            ˜^˜˜˜˜˜
./pat.h:1425:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1467:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1824:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:1829:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1847:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:1848:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:1871:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1892:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1898:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1887:21: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                patid = readCnt_-1;
                                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:1895:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:1897:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:1902:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2031:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2081:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2124:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2161:44: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(r2 != NULL) (*r2).nameBuf[nameLen] = c;
                                                              ˜ ^
./pat.h:2162:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:2165:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2168:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength((*r2).name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2175:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2179:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength((*r2).name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2172:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2174:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2177:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, (*r2).nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2208:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2209:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2240:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2264:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2276:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                c2 = c;
                                   ˜ ^
./pat.h:2284:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2286:25: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                c = charToPhred33(c, solQuals_, phred64Quals_);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2288:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.qualBuf[off] = c;
                                                               ˜ ^
./pat.h:2300:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2303:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        c2 = c;
                           ˜ ^
./pat.h:2332:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                nameChars_(0), bufCur_(0), subReadCnt_(0llu)
                                                       ^
./pat.h:2361:32: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                nameBuf_[nameChars_++] = c;
                                                                       ˜ ^
./pat.h:2379:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        buf_[bufCur_++] = c;
                                                        ˜ ^
./pat.h:2408:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
                                        itoa10(readCnt_ - subReadCnt_, &r.nameBuf[nameChars_]);
                                        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2414:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        patid = readCnt_-1;
                                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2574:28: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                r.nameBuf[nameLen++] = c;
                                                     ˜ ^
./pat.h:2578:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _setLength(r.name, nameLen);
                                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2586:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2608:18: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.primer = c;
                                                         ˜ ^
./pat.h:2609:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.trimc = c2;
                                                        ˜ ^˜
./pat.h:2664:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.patFw, dstLen);
                        ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:2683:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = qualsRead - mytrim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2702:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2731:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = (*qualsReadCur) - trim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2733:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        c = charToPhred33(c, solQuals_, phred64Quals_);
                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2735:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        qbuf[off] = c;
                                                                  ˜ ^
./pat.h:2755:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2792:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altPatFw[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜
./pat.h:2794:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altQual[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜
./pat.h:2816:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2813:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, r.nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2815:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                nameLen = strlen(r.nameBuf);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2822:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2929:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2930:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2944:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                size_t len = dstLen - mytrim5;
                                       ˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2959:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2961:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2973:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2970:10: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                itoa10(readCnt_, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2972:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                nameLen = strlen(r.nameBuf);
                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2976:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:3062:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
pat.cpp:62:34: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.qualBuf[qualsRead++] = ('!' + num);
                                               ˜  ˜˜˜˜^˜˜˜˜
pat.cpp:73:43: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.qualBuf[qualsRead++] = charToPhred33(c, solexa64, phred64);
                                                 ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
pat.cpp:96:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        _setLength(r.qual, trimmedReadLen);
        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:77:16: note: in instantiation of function template specialization 'seqan::length<char, seqan::Alloc<void> >' requested here
        size_t plen = length(path);
                      ^
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./alphabet.h:144:19: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >' requested here
        size_t readLen = seqan::length(read);
                         ^
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<char>' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<char>' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<char>' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<char>' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<char, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<char, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<char, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:278:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<char, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(name, sz);
                ^
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<seqan::SimpleType<unsigned char, seqan::_Dna5>, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:283:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(seq, sz);
                ^
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:90:
SeqAn-1.1/seqan/basic/basic_iterator_adapt_std.h:307:67: warning: implicit conversion changes signedness: 'unsigned long' to 'const difference_type' (aka 'const long') [-Wsign-conversion]
        return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) + right);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:764:76: note: in instantiation of function template specialization 'seqan::operator+<const std::basic_string<char>, unsigned long>' requested here
                        arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
                                                                                                ^
SeqAn-1.1/seqan/sequence/string_base.h:812:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, const std::basic_string<char> >' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:737:2: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char>, seqan::TagGenerous_>' requested here
        assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:70:3: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char> >' requested here
                assign(*this, source);
                ^
./pat.h:1391:17: note: in instantiation of function template specialization 'seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >::String<std::basic_string<char> >' requested here
                        v_.push_back(s);
                                     ^
148 warnings generated.
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:52:
SeqAn-1.1/seqan/basic/basic_profile.h:161:14: warning: implicit conversion changes signedness: '_proInt' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
        return (_proData<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:54:
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:70:22: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
        const int DEFAULT = ˜(˜0u >> 1); // initialize with the smallest int
                  ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:229:116: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
                finline static void run(unsigned char* ptr, unsigned char c) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
                                                                                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1131:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1140:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char)c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1149:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1167:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1178:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna5<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1187:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1196:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1205:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna5<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1226:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Iupac<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1235:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1244:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1251:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1258:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1269:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_AA<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1278:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1287:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:46:
SeqAn-1.1/seqan/file/cstream.h:142:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return getc(source);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:170:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:181:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:193:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
SeqAn-1.1/seqan/file/cstream.h:205:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:12:
In file included from ./alphabet.h:9:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:14:
In file included from ./threading.h:5:
./tinythread.h:631:9: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
typedef long long __intmax_t;
        ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:15:
./bitset.h:23:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                sz &= ˜31;            // Make sure it's 32-aligned
                   ˜˜ ^˜˜
./bitset.h:511:17: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        oss << (test(i)? "1" : "0");
                                ˜˜˜˜ ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:17:
In file included from ./pat.h:18:
./filebuf.h:73:61: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(_lastn_cur < LASTN_BUF_SZ) _lastn_buf[_lastn_cur++] = c;
                                                                               ˜ ^
./filebuf.h:158:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _inf->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:161:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _ins->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:478:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = slen;
                                     ˜ ^˜˜˜
./filebuf.h:505:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = len;
                                     ˜ ^˜˜
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:17:
In file included from ./pat.h:19:
./qual.h:93:40: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
                char cc = solexaToPhred((int)c - 64) + 33;
                     ˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./qual.h:147:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return (int)pQ;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜
./qual.h:161:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:165:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./qual.h:188:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:191:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:17:
In file included from ./pat.h:20:
In file included from ./hit_set.h:16:
./edit.h:36:7: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                   ˜^˜
./edit.h:36:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                      ˜^˜
./edit.h:36:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                               ˜^˜
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:17:
In file included from ./pat.h:20:
./hit_set.h:37:12: warning: implicit conversion changes signedness: 'const uint8_t' (aka 'const unsigned char') to 'char' [-Wsign-conversion]
                fb.write(fw);
                ˜˜       ^˜
./hit_set.h:44:17: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t sz = edits.size();
                         ˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:50:8: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                sz = cedits.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:63:8: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                fw = fb.get();
                   ˜ ^˜˜˜˜˜˜˜
./hit_set.h:65:13: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                stratum = fb.get();
                        ˜ ^˜˜˜˜˜˜˜
./hit_set.h:244:16: warning: implicit conversion loses integer precision: 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t i = seqan::length(name);
                         ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:248:7: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = seqan::length(seq);
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:256:7: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = ents.size();
                  ˜ ^˜˜˜˜˜˜˜˜˜˜
./hit_set.h:298:18: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                maxedStratum = fb.get();
                             ˜ ^˜˜˜˜˜˜˜
./hit_set.h:391:29: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                ents.erase(ents.begin() + i);
                           ˜˜˜˜           ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:17:
./pat.h:53:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:61:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:70:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:167:10: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                return seqan::length(patFw);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:723:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t ret = 0llu;
                               ^
./pat.h:728:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                return make_pair(ret, 0llu);
                                      ^
./pat.h:875:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                ^
./pat.h:875:32: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                             ^
./pat.h:1087:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1105:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1126:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, length);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1128:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, length);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:1129:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                itoa10(patid, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜
./pat.h:1164:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1169:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1183:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                patid_ += numthreads_;
                       ˜˜ ^˜˜˜˜˜˜˜˜˜˜
./pat.h:1188:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1189:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1358:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        s.erase(0, mytrim5);
                                        ˜          ^˜˜˜˜˜˜
./pat.h:1362:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        s.erase(s.length()-trim3_);
                                                          ˜^˜˜˜˜˜
./pat.h:1374:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        vq.erase(0, mytrim5);
                                        ˜˜          ^˜˜˜˜˜˜
./pat.h:1378:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        vq.erase(vq.length()-trim3_);
                                                            ˜^˜˜˜˜˜
./pat.h:1425:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1467:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1824:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:1829:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1847:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:1848:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:1871:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1892:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1898:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1887:21: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                patid = readCnt_-1;
                                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:1895:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:1897:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:1902:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2031:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2081:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2124:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2161:44: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(r2 != NULL) (*r2).nameBuf[nameLen] = c;
                                                              ˜ ^
./pat.h:2162:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:2165:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2168:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength((*r2).name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2175:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2179:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength((*r2).name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2172:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2174:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2177:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, (*r2).nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2208:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2209:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2240:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2264:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2276:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                c2 = c;
                                   ˜ ^
./pat.h:2284:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2286:25: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                c = charToPhred33(c, solQuals_, phred64Quals_);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2288:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.qualBuf[off] = c;
                                                               ˜ ^
./pat.h:2300:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2303:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        c2 = c;
                           ˜ ^
./pat.h:2332:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                nameChars_(0), bufCur_(0), subReadCnt_(0llu)
                                                       ^
./pat.h:2361:32: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                nameBuf_[nameChars_++] = c;
                                                                       ˜ ^
./pat.h:2379:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        buf_[bufCur_++] = c;
                                                        ˜ ^
./pat.h:2408:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
                                        itoa10(readCnt_ - subReadCnt_, &r.nameBuf[nameChars_]);
                                        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2414:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        patid = readCnt_-1;
                                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2574:28: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                r.nameBuf[nameLen++] = c;
                                                     ˜ ^
./pat.h:2578:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _setLength(r.name, nameLen);
                                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2586:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2608:18: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.primer = c;
                                                         ˜ ^
./pat.h:2609:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.trimc = c2;
                                                        ˜ ^˜
./pat.h:2664:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.patFw, dstLen);
                        ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:2683:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = qualsRead - mytrim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2702:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2731:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = (*qualsReadCur) - trim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2733:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        c = charToPhred33(c, solQuals_, phred64Quals_);
                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2735:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        qbuf[off] = c;
                                                                  ˜ ^
./pat.h:2755:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2792:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altPatFw[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜
./pat.h:2794:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altQual[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜
./pat.h:2816:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2813:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, r.nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2815:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                nameLen = strlen(r.nameBuf);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2822:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2929:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2930:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2944:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                size_t len = dstLen - mytrim5;
                                       ˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2959:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2961:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2973:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2970:10: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                itoa10(readCnt_, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2972:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                nameLen = strlen(r.nameBuf);
                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2976:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:3062:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
./hit.h:181:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                memset(ents_, 0, len_ << 2);
                                ˜˜˜˜˜˜           ˜˜˜˜˜^˜˜˜
./hit.h:204:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                ii = h.length() - ii - 1;
                                                ˜ ^˜
./hit.h:208:18: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        if(h.mms.test(i)) {
                           ˜          ^
./hit.h:209:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                rc = charToDna5[(int)h.refcs[i]];
                                                     ˜       ^
./hit.h:204:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                                ii = h.length() - ii - 1;
                                   ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./hit.h:316:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numAligned_(0llu),
                            ^
./hit.h:317:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numUnaligned_(0llu),
                              ^
./hit.h:318:13: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numMaxed_(0llu),
                          ^
./hit.h:319:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numReported_(0llu),
                             ^
./hit.h:320:22: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numReportedPaired_(0llu),
                                   ^
./hit.h:421:22: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                        sort(hs.begin() + start, hs.begin() + end);
                             ˜˜           ^˜˜˜˜
./hit.h:421:42: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                        sort(hs.begin() + start, hs.begin() + end);
                                                 ˜˜           ^˜˜
./hit.h:438:35: warning: implicit conversion changes signedness: 'streamoff' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        out(h.h.first).writeChars(buf, ss.tellp());
                        ˜˜˜                            ^˜˜˜˜˜˜˜˜˜
./hit.h:623:51: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:625:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:647:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:648:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:650:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:651:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:677:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:679:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:699:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:700:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:702:58: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:703:58: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:730:52: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:732:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:752:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:753:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:755:57: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:756:57: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:971:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                _numValidHits(0llu),
                              ^
./hit.h:1021:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        ret = _bufferedHits.size();
                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:1336:40: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        _bufferedHits[i].oms = (sz / mult_) - 1;
                                             ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./hit.h:1519:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                ss << "<" << h.h.first << "," << (h.h.second + offBase) << "," << h.mms.count();
                                                             ˜ ^˜˜˜˜˜˜
In file included from ebwt_search_util.cpp:1:
./ebwt_search_util.h:202:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                        al.u64.u64 = 0xffffffffffffffffllu;
                                     ^
./ebwt_search_util.h:266:26: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        uint32_t off = al.off.off;
                                 ˜˜˜   ˜˜˜˜˜˜˜^˜˜
./ebwt_search_util.h:324:26: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                uint16_t tpos0 = plen-1-pos0;
                         ˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜
./ebwt_search_util.h:330:51: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                appendValue(muts, QueryMutation(tpos0, oldChar, chr0)); // apply mutation
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜
./ebwt_search_util.h:335:27: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        uint16_t tpos1 = plen-1-pos1;
                                 ˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜
./ebwt_search_util.h:342:52: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                        appendValue(muts, QueryMutation(tpos1, oldChar, chr1)); // apply mutation
                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜
./ebwt_search_util.h:347:28: warning: implicit conversion loses integer precision: 'unsigned int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                                uint16_t tpos2 = plen-1-pos2;
                                         ˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜
./ebwt_search_util.h:355:48: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                                append(muts, QueryMutation(tpos2, oldChar, chr2)); // apply mutation
                                             ˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜
./ebwt_search_util.h:317:19: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t plen = length(seq);
                         ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
ebwt_search_util.cpp:31:39: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        cout << os[h.h.first][h.h.second + i];
                                                         ˜ ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:77:16: note: in instantiation of function template specialization 'seqan::length<char, seqan::Alloc<void> >' requested here
        size_t plen = length(path);
                      ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./alphabet.h:144:19: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >' requested here
        size_t readLen = seqan::length(read);
                         ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<char>' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<char>' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<char>' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<char>' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<char, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<char, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<char, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:278:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<char, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(name, sz);
                ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<seqan::SimpleType<unsigned char, seqan::_Dna5>, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:283:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(seq, sz);
                ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:90:
SeqAn-1.1/seqan/basic/basic_iterator_adapt_std.h:307:67: warning: implicit conversion changes signedness: 'unsigned long' to 'const difference_type' (aka 'const long') [-Wsign-conversion]
        return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) + right);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:764:76: note: in instantiation of function template specialization 'seqan::operator+<const std::basic_string<char>, unsigned long>' requested here
                        arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
                                                                                                ^
SeqAn-1.1/seqan/sequence/string_base.h:812:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, const std::basic_string<char> >' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:737:2: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char>, seqan::TagGenerous_>' requested here
        assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:70:3: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char> >' requested here
                assign(*this, source);
                ^
./pat.h:1391:17: note: in instantiation of function template specialization 'seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >::String<std::basic_string<char> >' requested here
                        v_.push_back(s);
                                     ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:415:50: warning: implicit conversion changes signedness: 'int' to 'typename Size<String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        if (old_capacity >= (TSize)new_capacity) return new_capacity;
                                                 ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/sequence_interface.h:1325:9: note: in instantiation of function template specialization 'seqan::reserve<QueryMutation, void, int, seqan::TagExact_>' requested here
        return reserve(me, new_capacity, typename DefaultOverflowExplicit<T>::Type());
               ^
./ebwt_search_util.h:315:3: note: in instantiation of function template specialization 'seqan::reserve<seqan::String<QueryMutation, seqan::Alloc<void> >, int>' requested here
                reserve(muts, 4);
                ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:418:94: warning: implicit conversion changes signedness: 'int' to 'typename Size<String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        typename Value< String<TValue, Alloc<TSpec> > >::Type * old_array = _reallocateStorage(seq, new_capacity, tag);
                                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_alloc.h:430:9: warning: implicit conversion changes signedness: 'int' to 'typename Size<String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return new_capacity;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<QueryMutation, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/sequence/string_alloc.h:417:21: note: in instantiation of function template specialization 'seqan::length<QueryMutation, seqan::Alloc<void> >' requested here
        TSize seq_length = length(seq);
                           ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1325:9: note: in instantiation of function template specialization 'seqan::reserve<QueryMutation, void, int, seqan::TagExact_>' requested here
        return reserve(me, new_capacity, typename DefaultOverflowExplicit<T>::Type());
               ^
./ebwt_search_util.h:315:3: note: in instantiation of function template specialization 'seqan::reserve<seqan::String<QueryMutation, seqan::Alloc<void> >, int>' requested here
                reserve(muts, 4);
                ^
196 warnings generated.
In file included from log.cpp:5:
In file included from ./log.h:5:
In file included from ./threading.h:5:
./tinythread.h:631:9: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
typedef long long __intmax_t;
        ^
1 warning generated.
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:52:
SeqAn-1.1/seqan/basic/basic_profile.h:161:14: warning: implicit conversion changes signedness: '_proInt' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
        return (_proData<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:54:
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:70:22: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
        const int DEFAULT = ˜(˜0u >> 1); // initialize with the smallest int
                  ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:229:116: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
                finline static void run(unsigned char* ptr, unsigned char c) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
                                                                                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1131:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1140:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char)c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1149:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1167:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1178:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna5<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1187:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1196:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1205:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna5<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1226:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Iupac<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1235:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1244:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1251:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1258:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1269:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_AA<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1278:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1287:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from hit_set.cpp:11:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:46:
SeqAn-1.1/seqan/file/cstream.h:142:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return getc(source);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:170:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:181:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:193:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
SeqAn-1.1/seqan/file/cstream.h:205:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
In file included from hit_set.cpp:11:
In file included from ./alphabet.h:9:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from hit_set.cpp:12:
In file included from ./hit_set.h:15:
./filebuf.h:73:61: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(_lastn_cur < LASTN_BUF_SZ) _lastn_buf[_lastn_cur++] = c;
                                                                               ˜ ^
./filebuf.h:158:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _inf->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:161:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _ins->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:478:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = slen;
                                     ˜ ^˜˜˜
./filebuf.h:505:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = len;
                                     ˜ ^˜˜
In file included from hit_set.cpp:12:
In file included from ./hit_set.h:16:
./edit.h:36:7: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                   ˜^˜
./edit.h:36:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                      ˜^˜
./edit.h:36:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                               ˜^˜
In file included from hit_set.cpp:12:
./hit_set.h:37:12: warning: implicit conversion changes signedness: 'const uint8_t' (aka 'const unsigned char') to 'char' [-Wsign-conversion]
                fb.write(fw);
                ˜˜       ^˜
./hit_set.h:44:17: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t sz = edits.size();
                         ˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:50:8: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                sz = cedits.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:63:8: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                fw = fb.get();
                   ˜ ^˜˜˜˜˜˜˜
./hit_set.h:65:13: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                stratum = fb.get();
                        ˜ ^˜˜˜˜˜˜˜
./hit_set.h:244:16: warning: implicit conversion loses integer precision: 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t i = seqan::length(name);
                         ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:248:7: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = seqan::length(seq);
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:256:7: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = ents.size();
                  ˜ ^˜˜˜˜˜˜˜˜˜˜
./hit_set.h:298:18: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                maxedStratum = fb.get();
                             ˜ ^˜˜˜˜˜˜˜
./hit_set.h:391:29: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                ents.erase(ents.begin() + i);
                           ˜˜˜˜           ^
hit_set.cpp:25:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                const HitSetEnt& h = ents[i];
                                     ˜˜˜˜ ^
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:77:16: note: in instantiation of function template specialization 'seqan::length<char, seqan::Alloc<void> >' requested here
        size_t plen = length(path);
                      ^
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./alphabet.h:144:19: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >' requested here
        size_t readLen = seqan::length(read);
                         ^
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<char>' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<char>' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<char>' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<char>' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<char, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<char, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<char, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:278:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<char, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(name, sz);
                ^
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<seqan::SimpleType<unsigned char, seqan::_Dna5>, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:283:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(seq, sz);
                ^
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:323:17: warning: implicit conversion loses integer precision: 'const int' to 'unsigned char' [-Wconversion]
        target.value = source;
                     ˜ ^˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:82:3: note: in instantiation of function template specialization 'seqan::assign<unsigned char, seqan::_Dna5, int>' requested here
                assign(*this, other);
                ^
./alphabet.h:69:11: note: in instantiation of function template specialization 'seqan::SimpleType<unsigned char, seqan::_Dna5>::SimpleType<int>' requested here
                        s[i] = (TVal)4;
                               ^
hit_set.cpp:29:4: note: in instantiation of function template specialization 'reverseComplementInPlace<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >' requested here
                        reverseComplementInPlace(seqrc, color);
                        ^
49 warnings generated.
In file included from refmap.cpp:10:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
1 warning generated.
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:52:
SeqAn-1.1/seqan/basic/basic_profile.h:161:14: warning: implicit conversion changes signedness: '_proInt' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
        return (_proData<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:54:
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:70:22: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
        const int DEFAULT = ˜(˜0u >> 1); // initialize with the smallest int
                  ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:229:116: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
                finline static void run(unsigned char* ptr, unsigned char c) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
                                                                                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1131:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1140:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char)c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1149:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1167:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1178:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna5<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1187:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1196:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1205:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna5<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1226:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Iupac<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1235:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1244:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1251:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1258:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1269:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_AA<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1278:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1287:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from sam.cpp:11:
In file included from ./pat.h:13:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:46:
SeqAn-1.1/seqan/file/cstream.h:142:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return getc(source);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:170:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:181:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:193:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
SeqAn-1.1/seqan/file/cstream.h:205:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
In file included from sam.cpp:11:
In file included from ./pat.h:13:
In file included from ./alphabet.h:9:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from sam.cpp:11:
In file included from ./pat.h:17:
In file included from ./threading.h:5:
./tinythread.h:631:9: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
typedef long long __intmax_t;
        ^
In file included from sam.cpp:11:
In file included from ./pat.h:18:
./filebuf.h:73:61: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(_lastn_cur < LASTN_BUF_SZ) _lastn_buf[_lastn_cur++] = c;
                                                                               ˜ ^
./filebuf.h:158:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _inf->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:161:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _ins->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:478:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = slen;
                                     ˜ ^˜˜˜
./filebuf.h:505:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = len;
                                     ˜ ^˜˜
In file included from sam.cpp:11:
In file included from ./pat.h:19:
./qual.h:93:40: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
                char cc = solexaToPhred((int)c - 64) + 33;
                     ˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./qual.h:147:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return (int)pQ;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜
./qual.h:161:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:165:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./qual.h:188:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:191:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from sam.cpp:11:
In file included from ./pat.h:20:
In file included from ./hit_set.h:16:
./edit.h:36:7: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                   ˜^˜
./edit.h:36:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                      ˜^˜
./edit.h:36:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                               ˜^˜
In file included from sam.cpp:11:
In file included from ./pat.h:20:
./hit_set.h:37:12: warning: implicit conversion changes signedness: 'const uint8_t' (aka 'const unsigned char') to 'char' [-Wsign-conversion]
                fb.write(fw);
                ˜˜       ^˜
./hit_set.h:44:17: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t sz = edits.size();
                         ˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:50:8: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                sz = cedits.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:63:8: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                fw = fb.get();
                   ˜ ^˜˜˜˜˜˜˜
./hit_set.h:65:13: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                stratum = fb.get();
                        ˜ ^˜˜˜˜˜˜˜
./hit_set.h:244:16: warning: implicit conversion loses integer precision: 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t i = seqan::length(name);
                         ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:248:7: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = seqan::length(seq);
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:256:7: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = ents.size();
                  ˜ ^˜˜˜˜˜˜˜˜˜˜
./hit_set.h:298:18: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                maxedStratum = fb.get();
                             ˜ ^˜˜˜˜˜˜˜
./hit_set.h:391:29: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                ents.erase(ents.begin() + i);
                           ˜˜˜˜           ^
In file included from sam.cpp:11:
./pat.h:53:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:61:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:70:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:167:10: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                return seqan::length(patFw);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:723:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t ret = 0llu;
                               ^
./pat.h:728:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                return make_pair(ret, 0llu);
                                      ^
./pat.h:875:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                ^
./pat.h:875:32: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                             ^
./pat.h:1087:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1105:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1126:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, length);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1128:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, length);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:1129:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                itoa10(patid, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜
./pat.h:1164:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1169:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1183:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                patid_ += numthreads_;
                       ˜˜ ^˜˜˜˜˜˜˜˜˜˜
./pat.h:1188:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1189:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1358:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        s.erase(0, mytrim5);
                                        ˜          ^˜˜˜˜˜˜
./pat.h:1362:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        s.erase(s.length()-trim3_);
                                                          ˜^˜˜˜˜˜
./pat.h:1374:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        vq.erase(0, mytrim5);
                                        ˜˜          ^˜˜˜˜˜˜
./pat.h:1378:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        vq.erase(vq.length()-trim3_);
                                                            ˜^˜˜˜˜˜
./pat.h:1425:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1467:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1824:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:1829:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1847:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:1848:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:1871:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1892:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1898:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1887:21: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                patid = readCnt_-1;
                                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:1895:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:1897:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:1902:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2031:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2081:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2124:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2161:44: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(r2 != NULL) (*r2).nameBuf[nameLen] = c;
                                                              ˜ ^
./pat.h:2162:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:2165:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2168:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength((*r2).name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2175:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2179:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength((*r2).name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2172:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2174:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2177:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, (*r2).nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2208:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2209:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2240:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2264:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2276:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                c2 = c;
                                   ˜ ^
./pat.h:2284:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2286:25: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                c = charToPhred33(c, solQuals_, phred64Quals_);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2288:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.qualBuf[off] = c;
                                                               ˜ ^
./pat.h:2300:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2303:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        c2 = c;
                           ˜ ^
./pat.h:2332:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                nameChars_(0), bufCur_(0), subReadCnt_(0llu)
                                                       ^
./pat.h:2361:32: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                nameBuf_[nameChars_++] = c;
                                                                       ˜ ^
./pat.h:2379:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        buf_[bufCur_++] = c;
                                                        ˜ ^
./pat.h:2408:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
                                        itoa10(readCnt_ - subReadCnt_, &r.nameBuf[nameChars_]);
                                        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2414:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        patid = readCnt_-1;
                                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2574:28: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                r.nameBuf[nameLen++] = c;
                                                     ˜ ^
./pat.h:2578:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _setLength(r.name, nameLen);
                                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2586:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2608:18: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.primer = c;
                                                         ˜ ^
./pat.h:2609:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.trimc = c2;
                                                        ˜ ^˜
./pat.h:2664:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.patFw, dstLen);
                        ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:2683:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = qualsRead - mytrim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2702:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2731:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = (*qualsReadCur) - trim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2733:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        c = charToPhred33(c, solQuals_, phred64Quals_);
                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2735:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        qbuf[off] = c;
                                                                  ˜ ^
./pat.h:2755:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2792:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altPatFw[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜
./pat.h:2794:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altQual[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜
./pat.h:2816:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2813:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, r.nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2815:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                nameLen = strlen(r.nameBuf);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2822:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2929:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2930:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2944:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                size_t len = dstLen - mytrim5;
                                       ˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2959:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2961:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2973:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2970:10: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                itoa10(readCnt_, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2972:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                nameLen = strlen(r.nameBuf);
                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2976:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:3062:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
In file included from sam.cpp:12:
In file included from ./hit.h:15:
./bitset.h:23:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                sz &= ˜31;            // Make sure it's 32-aligned
                   ˜˜ ^˜˜
./bitset.h:511:17: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        oss << (test(i)? "1" : "0");
                                ˜˜˜˜ ^
In file included from sam.cpp:12:
./hit.h:181:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                memset(ents_, 0, len_ << 2);
                                ˜˜˜˜˜˜           ˜˜˜˜˜^˜˜˜
./hit.h:204:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                ii = h.length() - ii - 1;
                                                ˜ ^˜
./hit.h:208:18: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        if(h.mms.test(i)) {
                           ˜          ^
./hit.h:209:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                rc = charToDna5[(int)h.refcs[i]];
                                                     ˜       ^
./hit.h:204:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                                ii = h.length() - ii - 1;
                                   ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./hit.h:316:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numAligned_(0llu),
                            ^
./hit.h:317:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numUnaligned_(0llu),
                              ^
./hit.h:318:13: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numMaxed_(0llu),
                          ^
./hit.h:319:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numReported_(0llu),
                             ^
./hit.h:320:22: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numReportedPaired_(0llu),
                                   ^
./hit.h:421:22: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                        sort(hs.begin() + start, hs.begin() + end);
                             ˜˜           ^˜˜˜˜
./hit.h:421:42: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                        sort(hs.begin() + start, hs.begin() + end);
                                                 ˜˜           ^˜˜
./hit.h:438:35: warning: implicit conversion changes signedness: 'streamoff' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        out(h.h.first).writeChars(buf, ss.tellp());
                        ˜˜˜                            ^˜˜˜˜˜˜˜˜˜
./hit.h:623:51: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:625:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:647:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:648:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:650:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:651:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:677:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:679:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:699:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:700:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:702:58: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:703:58: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:730:52: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:732:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:752:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:753:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:755:57: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:756:57: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:971:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                _numValidHits(0llu),
                              ^
./hit.h:1021:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        ret = _bufferedHits.size();
                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:1336:40: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        _bufferedHits[i].oms = (sz / mult_) - 1;
                                             ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./hit.h:1519:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                ss << "<" << h.h.first << "," << (h.h.second + offBase) << "," << h.mms.count();
                                                             ˜ ^˜˜˜˜˜˜
sam.cpp:164:17: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        if(mms->test(i)) {
                           ˜˜˜       ^
sam.cpp:168:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                char refChar = toupper((*refcs)[i]);
                                     ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sam.cpp:168:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                char refChar = toupper((*refcs)[i]);
                                                       ˜        ^
sam.cpp:179:17: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        if(mms->test(i)) {
                           ˜˜˜       ^
sam.cpp:183:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                char refChar = toupper((*refcs)[i]);
                                     ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sam.cpp:183:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                char refChar = toupper((*refcs)[i]);
                                                       ˜        ^
sam.cpp:178:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                for (int i = len-1; i >= 0; -- i) {
                         ˜   ˜˜˜^˜
sam.cpp:250:26: warning: implicit conversion changes signedness: 'streamoff' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                out(0).writeChars(buf, ss.tellp());
                ˜˜˜                    ^˜˜˜˜˜˜˜˜˜
sam.cpp:387:47: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                                                reportSamHits(hs, i, i+2, 0, hs.size()/2+1);
                                                ˜˜˜˜˜˜˜˜˜˜˜˜˜                ˜˜˜˜˜˜˜˜˜˜˜^˜
sam.cpp:402:52: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                        reportSamHit(hs[r], /*MAPQ*/0, /*XM:I*/hs.size()+1);
                        ˜˜˜˜˜˜˜˜˜˜˜˜                           ˜˜˜˜˜˜˜˜˜^˜
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:77:16: note: in instantiation of function template specialization 'seqan::length<char, seqan::Alloc<void> >' requested here
        size_t plen = length(path);
                      ^
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./alphabet.h:144:19: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >' requested here
        size_t readLen = seqan::length(read);
                         ^
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<char>' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<char>' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<char>' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<char>' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<char, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<char, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<char, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:278:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<char, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(name, sz);
                ^
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<seqan::SimpleType<unsigned char, seqan::_Dna5>, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:283:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(seq, sz);
                ^
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:90:
SeqAn-1.1/seqan/basic/basic_iterator_adapt_std.h:307:67: warning: implicit conversion changes signedness: 'unsigned long' to 'const difference_type' (aka 'const long') [-Wsign-conversion]
        return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) + right);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:764:76: note: in instantiation of function template specialization 'seqan::operator+<const std::basic_string<char>, unsigned long>' requested here
                        arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
                                                                                                ^
SeqAn-1.1/seqan/sequence/string_base.h:812:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, const std::basic_string<char> >' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:737:2: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char>, seqan::TagGenerous_>' requested here
        assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:70:3: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char> >' requested here
                assign(*this, source);
                ^
./pat.h:1391:17: note: in instantiation of function template specialization 'seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >::String<std::basic_string<char> >' requested here
                        v_.push_back(s);
                                     ^
192 warnings generated.
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:6:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:52:
SeqAn-1.1/seqan/basic/basic_profile.h:161:14: warning: implicit conversion changes signedness: '_proInt' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
        return (_proData<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:6:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:54:
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:70:22: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
        const int DEFAULT = ˜(˜0u >> 1); // initialize with the smallest int
                  ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:229:116: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
                finline static void run(unsigned char* ptr, unsigned char c) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
                                                                                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:6:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1131:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1140:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char)c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1149:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1167:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1178:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna5<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1187:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1196:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1205:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna5<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1226:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Iupac<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1235:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1244:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1251:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1258:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1269:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_AA<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1278:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1287:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:46:
SeqAn-1.1/seqan/file/cstream.h:142:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return getc(source);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:170:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:181:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:193:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
SeqAn-1.1/seqan/file/cstream.h:205:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:9:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from color_dec.cpp:14:
./qual.h:93:40: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
                char cc = solexaToPhred((int)c - 64) + 33;
                     ˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./qual.h:147:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return (int)pQ;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜
./qual.h:161:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:165:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./qual.h:188:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:191:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
color_dec.cpp:93:12: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                s[i--] = to; // install best nucleotide
                       ˜ ^˜
color_dec.cpp:194:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                const int refc = ref[refi + t];
                                          ˜ ^
color_dec.cpp:239:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                  read, readi, readi + t - 1,
                                     ˜ ^
color_dec.cpp:240:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                  ref, refi, refi + t,
                                  ˜ ^
color_dec.cpp:193:17: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                t = c - readi + 1;
                  ˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:6:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:77:16: note: in instantiation of function template specialization 'seqan::length<char, seqan::Alloc<void> >' requested here
        size_t plen = length(path);
                      ^
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:6:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./alphabet.h:144:19: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >' requested here
        size_t readLen = seqan::length(read);
                         ^
38 warnings generated.
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:52:
SeqAn-1.1/seqan/basic/basic_profile.h:161:14: warning: implicit conversion changes signedness: '_proInt' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
        return (_proData<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:54:
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:70:22: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
        const int DEFAULT = ˜(˜0u >> 1); // initialize with the smallest int
                  ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_metaprogramming.h:229:116: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
                finline static void run(unsigned char* ptr, unsigned char c) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
                                                                                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:106:
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1131:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1140:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char)c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1149:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1167:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1178:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Dna5<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1187:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1196:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1205:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Iupac_2_Dna5<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1226:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_Iupac<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1235:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1244:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1251:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1258:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1269:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Byte_2_AA<>::VALUE[c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1278:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:1287:17: warning: implicit conversion changes signedness: 'const char' to 'unsigned char' [-Wsign-conversion]
        target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from hit.cpp:1:
In file included from ./hit.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:46:
SeqAn-1.1/seqan/file/cstream.h:142:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return getc(source);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:170:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:181:9: warning: implicit conversion changes signedness: 'long' to 'Position<FILE *>::Type' (aka 'unsigned long') [-Wsign-conversion]
        return ::std::ftell(me);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:193:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
SeqAn-1.1/seqan/file/cstream.h:205:19: warning: implicit conversion changes signedness: 'Position<FILE *>::Type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
        ::std::fseek(me, pos, SEEK_SET);
        ˜˜               ^˜˜
In file included from hit.cpp:1:
In file included from ./hit.h:12:
In file included from ./alphabet.h:9:
./assert_helpers.h:23:22: warning: named variadic macros are a GNU extension [-Wvariadic-macros]
#define ASSERT_ONLY(x...)
                     ^
In file included from hit.cpp:1:
In file included from ./hit.h:14:
In file included from ./threading.h:5:
./tinythread.h:631:9: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
typedef long long __intmax_t;
        ^
In file included from hit.cpp:1:
In file included from ./hit.h:15:
./bitset.h:23:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                sz &= ˜31;            // Make sure it's 32-aligned
                   ˜˜ ^˜˜
./bitset.h:511:17: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        oss << (test(i)? "1" : "0");
                                ˜˜˜˜ ^
In file included from hit.cpp:1:
In file included from ./hit.h:17:
In file included from ./pat.h:18:
./filebuf.h:73:61: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(_lastn_cur < LASTN_BUF_SZ) _lastn_buf[_lastn_cur++] = c;
                                                                               ˜ ^
./filebuf.h:158:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _inf->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:161:16: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _buf_sz = _ins->gcount();
                                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./filebuf.h:478:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = slen;
                                     ˜ ^˜˜˜
./filebuf.h:505:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                cur_ = len;
                                     ˜ ^˜˜
In file included from hit.cpp:1:
In file included from ./hit.h:17:
In file included from ./pat.h:19:
./qual.h:93:40: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
                char cc = solexaToPhred((int)c - 64) + 33;
                     ˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./qual.h:147:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return (int)pQ;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜
./qual.h:161:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:165:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./qual.h:188:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
        uint8_t primQ = qual[off]; // qual of primary call
                ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜
./qual.h:191:18: warning: implicit conversion changes signedness: 'const typename Value<String<char, Alloc<void> > >::Type' (aka 'const char') to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                uint8_t altQ = altQual[i][off]; // qual of alt call
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from hit.cpp:1:
In file included from ./hit.h:17:
In file included from ./pat.h:20:
In file included from ./hit_set.h:16:
./edit.h:36:7: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                   ˜^˜
./edit.h:36:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                      ˜^˜
./edit.h:36:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chr(ch), qchr(0), type(ty), pos(po) { }
                                               ˜^˜
In file included from hit.cpp:1:
In file included from ./hit.h:17:
In file included from ./pat.h:20:
./hit_set.h:37:12: warning: implicit conversion changes signedness: 'const uint8_t' (aka 'const unsigned char') to 'char' [-Wsign-conversion]
                fb.write(fw);
                ˜˜       ^˜
./hit_set.h:44:17: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t sz = edits.size();
                         ˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:50:8: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                sz = cedits.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:63:8: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
                fw = fb.get();
                   ˜ ^˜˜˜˜˜˜˜
./hit_set.h:65:13: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                stratum = fb.get();
                        ˜ ^˜˜˜˜˜˜˜
./hit_set.h:244:16: warning: implicit conversion loses integer precision: 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                uint32_t i = seqan::length(name);
                         ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:248:7: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = seqan::length(seq);
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit_set.h:256:7: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                i = ents.size();
                  ˜ ^˜˜˜˜˜˜˜˜˜˜
./hit_set.h:298:18: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                maxedStratum = fb.get();
                             ˜ ^˜˜˜˜˜˜˜
./hit_set.h:391:29: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                ents.erase(ents.begin() + i);
                           ˜˜˜˜           ^
In file included from hit.cpp:1:
In file included from ./hit.h:17:
./pat.h:53:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:61:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:70:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                rseed ^= (p << off);
                      ˜˜  ˜˜^˜˜˜˜˜
./pat.h:167:10: warning: implicit conversion loses integer precision: 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                return seqan::length(patFw);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:723:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t ret = 0llu;
                               ^
./pat.h:728:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                return make_pair(ret, 0llu);
                                      ^
./pat.h:875:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                ^
./pat.h:875:32: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                uint64_t rets = 0llu, retp = 0llu;
                                             ^
./pat.h:1087:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1105:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1126:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, length);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1128:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, length);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:1129:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                itoa10(patid, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜
./pat.h:1164:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1169:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1183:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                patid_ += numthreads_;
                       ˜˜ ^˜˜˜˜˜˜˜˜˜˜
./pat.h:1188:12: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                patid_ = thread_;
                       ˜ ^˜˜˜˜˜˜
./pat.h:1189:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                rand_.init(thread_);
                ˜˜˜˜˜      ^˜˜˜˜˜˜
./pat.h:1358:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        s.erase(0, mytrim5);
                                        ˜          ^˜˜˜˜˜˜
./pat.h:1362:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        s.erase(s.length()-trim3_);
                                                          ˜^˜˜˜˜˜
./pat.h:1374:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        vq.erase(0, mytrim5);
                                        ˜˜          ^˜˜˜˜˜˜
./pat.h:1378:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        vq.erase(vq.length()-trim3_);
                                                            ˜^˜˜˜˜˜
./pat.h:1425:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1467:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_;
                      ˜ ^˜˜˜˜˜˜˜
./pat.h:1824:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:1829:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1847:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:1848:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:1871:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw, dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1892:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:1898:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:1887:21: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                patid = readCnt_-1;
                                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:1895:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:1897:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:1902:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2031:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2081:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2124:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2161:44: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if(r2 != NULL) (*r2).nameBuf[nameLen] = c;
                                                              ˜ ^
./pat.h:2162:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        r.nameBuf[nameLen++] = c;
                                             ˜ ^
./pat.h:2165:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2168:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength((*r2).name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2175:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2179:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength((*r2).name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜
./pat.h:2172:11: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                        itoa10(readCnt_, r.nameBuf);
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2174:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        nameLen = strlen(r.nameBuf);
                                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2177:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, (*r2).nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2208:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2209:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2240:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2264:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2276:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                c2 = c;
                                   ˜ ^
./pat.h:2284:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                size_t off = qualsRead - trim5;
                                                       ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2286:25: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                c = charToPhred33(c, solQuals_, phred64Quals_);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2288:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.qualBuf[off] = c;
                                                               ˜ ^
./pat.h:2300:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2303:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        c2 = c;
                           ˜ ^
./pat.h:2332:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                nameChars_(0), bufCur_(0), subReadCnt_(0llu)
                                                       ^
./pat.h:2361:32: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                nameBuf_[nameChars_++] = c;
                                                                       ˜ ^
./pat.h:2379:24: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        buf_[bufCur_++] = c;
                                                        ˜ ^
./pat.h:2408:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
                                        itoa10(readCnt_ - subReadCnt_, &r.nameBuf[nameChars_]);
                                        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2414:22: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                        patid = readCnt_-1;
                                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2574:28: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                r.nameBuf[nameLen++] = c;
                                                     ˜ ^
./pat.h:2578:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        _setLength(r.name, nameLen);
                                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2586:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.name, nameLen);
                        ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2608:18: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.primer = c;
                                                         ˜ ^
./pat.h:2609:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                r.trimc = c2;
                                                        ˜ ^˜
./pat.h:2664:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        _setLength(r.patFw, dstLen);
                        ˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜
./pat.h:2683:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = qualsRead - mytrim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2702:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2731:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                        size_t off = (*qualsReadCur) - trim5;
                                                               ˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
./pat.h:2733:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        c = charToPhred33(c, solQuals_, phred64Quals_);
                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./pat.h:2735:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                                        qbuf[off] = c;
                                                                  ˜ ^
./pat.h:2755:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.qual, dstLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2792:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altPatFw[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜
./pat.h:2794:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                _setLength(r.altQual[i-1], dstLen);
                                                ˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜
./pat.h:2816:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                _setLength(r.name, nameLen);
                                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2813:12: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                                itoa10(readCnt_, r.nameBuf);
                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2815:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                nameLen = strlen(r.nameBuf);
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2822:20: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        patid = readCnt_-1;
                              ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:2929:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.primer = c;
                                                 ˜ ^
./pat.h:2930:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        r.trimc = c2;
                                                ˜ ^˜
./pat.h:2944:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                size_t len = dstLen - mytrim5;
                                       ˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./pat.h:2959:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.patFw,  dstLen);
                ˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
./pat.h:2961:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.qual, dstLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜
./pat.h:2973:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                _setLength(r.name, nameLen);
                ˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
./pat.h:2970:10: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
                itoa10(readCnt_, r.nameBuf);
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
./pat.h:2972:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                nameLen = strlen(r.nameBuf);
                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./pat.h:2976:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
./pat.h:3062:19: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                patid = readCnt_-1;
                      ˜ ˜˜˜˜˜˜˜˜^˜
In file included from hit.cpp:1:
./hit.h:181:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                memset(ents_, 0, len_ << 2);
                                ˜˜˜˜˜˜           ˜˜˜˜˜^˜˜˜
./hit.h:204:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                ii = h.length() - ii - 1;
                                                ˜ ^˜
./hit.h:208:18: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        if(h.mms.test(i)) {
                           ˜          ^
./hit.h:209:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                rc = charToDna5[(int)h.refcs[i]];
                                                     ˜       ^
./hit.h:204:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                                ii = h.length() - ii - 1;
                                   ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./hit.h:316:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numAligned_(0llu),
                            ^
./hit.h:317:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numUnaligned_(0llu),
                              ^
./hit.h:318:13: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numMaxed_(0llu),
                          ^
./hit.h:319:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numReported_(0llu),
                             ^
./hit.h:320:22: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                numReportedPaired_(0llu),
                                   ^
./hit.h:421:22: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                        sort(hs.begin() + start, hs.begin() + end);
                             ˜˜           ^˜˜˜˜
./hit.h:421:42: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                        sort(hs.begin() + start, hs.begin() + end);
                                                 ˜˜           ^˜˜
./hit.h:438:35: warning: implicit conversion changes signedness: 'streamoff' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        out(h.h.first).writeChars(buf, ss.tellp());
                        ˜˜˜                            ^˜˜˜˜˜˜˜˜˜
./hit.h:623:51: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:625:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:647:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:648:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpAl_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:650:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:651:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpAlQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:677:53: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:679:56: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:699:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:700:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpUnal_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:702:58: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:703:58: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpUnalQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:730:52: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:732:55: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:752:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_1_->write(p.bufa().readOrigBuf, p.bufa().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:753:54: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                dumpMax_2_->write(p.bufb().readOrigBuf, p.bufb().readOrigBufLen);
                                ˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:755:57: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_1_->write(p.bufa().qualOrigBuf, p.bufa().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:756:57: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'streamsize' (aka 'long') [-Wsign-conversion]
                                        dumpMaxQv_2_->write(p.bufb().qualOrigBuf, p.bufb().qualOrigBufLen);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜                              ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:971:17: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                _numValidHits(0llu),
                              ^
./hit.h:1021:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        ret = _bufferedHits.size();
                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./hit.h:1336:40: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        _bufferedHits[i].oms = (sz / mult_) - 1;
                                             ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./hit.h:1519:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                ss << "<" << h.h.first << "," << (h.h.second + offBase) << "," << h.mms.count();
                                                             ˜ ^˜˜˜˜˜˜
hit.cpp:43:42: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                                                hs[i].oms = hs[i+1].oms = hs.size()/2;
                                                                        ˜ ˜˜˜˜˜˜˜˜˜^˜
hit.cpp:60:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        h.oms = hs.size();
                              ˜ ^˜˜˜˜˜˜˜˜
hit.cpp:116:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                pdiv = (h.h.second + offBase) / pospart;
                                                   ˜ ^˜˜˜˜˜˜
hit.cpp:116:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                pdiv = (h.h.second + offBase) / pospart;
                                                              ˜ ^˜˜˜˜˜˜
hit.cpp:117:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                pmod = (h.h.second + offBase) % pospart;
                                                   ˜ ^˜˜˜˜˜˜
hit.cpp:117:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                pmod = (h.h.second + offBase) % pospart;
                                                              ˜ ^˜˜˜˜˜˜
hit.cpp:122:30: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        ss2 << (pdiv + (dospill ? spillAmt : 0));
                                     ˜            ^˜˜˜˜˜˜˜
hit.cpp:124:61: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                           (pmod + h.length()) >= ((uint32_t)pospart * (spillAmt + 1))) {
                                                                     ˜  ˜˜˜˜˜˜˜˜˜^˜˜
hit.cpp:151:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                ss3 << (h.h.second + offBase);
                                                   ˜ ^˜˜˜˜˜˜
hit.cpp:191:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                ss << (h.h.second + offBase);
                                                  ˜ ^˜˜˜˜˜˜
hit.cpp:249:21: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                        char refChar = toupper(h.refcs[i]);
                                             ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
hit.cpp:254:30: warning: implicit conversion changes signedness: 'unsigned int' to 'const key_type' (aka 'const int') [-Wsign-conversion]
                                } else if(snpAnnots.find(i) != snpAnnots.end()) {
                                          ˜˜˜˜˜˜˜˜˜      ^
hit.cpp:258:30: warning: implicit conversion changes signedness: 'unsigned int' to 'const key_type' (aka 'const int') [-Wsign-conversion]
                                        ss << "S:" << snpAnnots[i] << ">" << qryChar;
                                                      ˜˜˜˜˜˜˜˜˜ ^
hit.cpp:100:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:129:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:147:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:158:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:166:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:171:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:176:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:188:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:195:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                if(!suppress.test(field++)) {
                    ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:202:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                if(!suppress.test(field++)) {
                    ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:209:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                if(!suppress.test(field++)) {
                    ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:214:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                if(!suppress.test(field++)) {
                    ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:238:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
                                        snpAnnots[off] = ai->second.second;
                                        ˜˜˜˜˜˜˜˜˜ ^˜˜
hit.cpp:266:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:272:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:299:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:305:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
hit.cpp:313:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        if(!suppress.test(field++)) {
                            ˜˜˜˜˜˜˜˜      ˜˜˜˜˜^˜
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<char, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SeqAn-1.1/seqan/file/cstream.h:77:16: note: in instantiation of function template specialization 'seqan::length<char, seqan::Alloc<void> >' requested here
        size_t plen = length(path);
                      ^
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:181:29: warning: implicit conversion changes signedness: 'long' to 'typename Size<const String<SimpleType<unsigned char, _Dna5>, Alloc<void> > >::Type' (aka 'unsigned long') [-Wsign-conversion]
        return end(me, Standard()) - begin(me, Standard());
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./alphabet.h:144:19: note: in instantiation of function template specialization 'seqan::length<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >' requested here
        size_t readLen = seqan::length(read);
                         ^
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<char>' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<char>' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<char>' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<char>' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<char, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<char, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<char, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:278:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<char, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(name, sz);
                ^
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:101:
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:50: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
                                             ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:2: note: in instantiation of function template specialization 'seqan::_arrayCopyForward_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:2: note: in instantiation of function template specialization 'seqan::arrayCopyForward<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        arrayCopyForward(source_begin, source_end, target_begin);
        ^
SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:2: note: in instantiation of function template specialization 'seqan::_arrayConstructCopy_Pointer<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
        _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:421:3: note: in instantiation of function template specialization 'seqan::arrayConstructCopy<seqan::SimpleType<unsigned char, seqan::_Dna5> >' requested here
                arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
                ^
SeqAn-1.1/seqan/sequence/string_base.h:1433:26: note: in instantiation of function template specialization 'seqan::reserve<seqan::SimpleType<unsigned char, seqan::_Dna5>, void, unsigned long, seqan::TagExact_>' requested here
                                TSize new_capacity = reserve(me, new_length, TExpand());
                                                     ^
SeqAn-1.1/seqan/sequence/string_base.h:1459:9: note: in instantiation of function template specialization 'seqan::_Resize_String<const seqan::Tag<seqan::TagExact_> >::resize_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> > >' requested here
        return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
               ^
SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:9: note: in instantiation of function template specialization 'seqan::resize<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, unsigned int, seqan::TagExact_>' requested here
        return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
               ^
./hit_set.h:283:3: note: in instantiation of function template specialization 'seqan::resize<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, unsigned int>' requested here
                seqan::resize(seq, sz);
                ^
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:90:
SeqAn-1.1/seqan/basic/basic_iterator_adapt_std.h:307:67: warning: implicit conversion changes signedness: 'unsigned long' to 'const difference_type' (aka 'const long') [-Wsign-conversion]
        return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) + right);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜
SeqAn-1.1/seqan/sequence/string_base.h:764:76: note: in instantiation of function template specialization 'seqan::operator+<const std::basic_string<char>, unsigned long>' requested here
                        arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
                                                                                                ^
SeqAn-1.1/seqan/sequence/string_base.h:812:2: note: in instantiation of function template specialization 'seqan::_Assign_String<const seqan::Tag<seqan::TagGenerous_> >::assign_<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, const std::basic_string<char> >' requested here
        _Assign_String<Tag<TExpand> const>::assign_(target, source);
        ^
SeqAn-1.1/seqan/sequence/string_base.h:737:2: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char>, seqan::TagGenerous_>' requested here
        assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
        ^
SeqAn-1.1/seqan/sequence/string_alloc.h:70:3: note: in instantiation of function template specialization 'seqan::assign<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>, std::basic_string<char> >' requested here
                assign(*this, source);
                ^
./pat.h:1391:17: note: in instantiation of function template specialization 'seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >::String<std::basic_string<char> >' requested here
                        v_.push_back(s);
                                     ^
213 warnings generated.
bowtie_main.cpp:46:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        lastret = bowtie(args.size(), myargs);
                                  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
1 warning generated.
mkdir -p ../inst
cp bowtie ../inst/bowtie
cp bowtie-build ../inst/bowtie-build
cd SpliceMap; \
	make -f Makefile; \
	echo "MAKE of SpliceMap DONE"	
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
SpliceMap_utils_QuasR.cpp:381:18: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        smallest_left = it->chr_end.back();
                      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:382:17: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        biggest_left = it->chr_end.back();
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:387:14: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                int temp = it->chr_end.back();
                    ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:582:21: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
                                M_end = *end_it + (*next_chr_start_it - *chr_end_it - 1);
                                      ˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:660:54: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                        start_end.read_start.push_back(suffix[suffix_idx].first);
                        ˜˜˜˜˜˜˜˜˜                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
SpliceMap_utils_QuasR.cpp:660:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        start_end.read_start.push_back(suffix[suffix_idx].first);
                                                       ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:662:74: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                        start_end.read_start.push_back(suffix[suffix_idx].second + good_it->d + 1); 
                        ˜˜˜˜˜˜˜˜˜                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
SpliceMap_utils_QuasR.cpp:662:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        start_end.read_start.push_back(suffix[suffix_idx].second + good_it->d + 1); 
                                                       ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:669:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        read_back_pos = suffix[suffix_idx].second;
                                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:673:53: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                start_end.read_start.push_back(suffix[suffix_idx].first);
                ˜˜˜˜˜˜˜˜˜                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
SpliceMap_utils_QuasR.cpp:673:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                start_end.read_start.push_back(suffix[suffix_idx].first);
                                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:679:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        read_back_pos = suffix[suffix_idx].second;
                                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:685:53: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                start_end.read_start.push_back(suffix[suffix_idx].first);
                ˜˜˜˜˜˜˜˜˜                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
SpliceMap_utils_QuasR.cpp:685:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                start_end.read_start.push_back(suffix[suffix_idx].first);
                                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:688:58: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                start_end.read_end.push_back(suffix[suffix_idx].second - good_it->d);  
                ˜˜˜˜˜˜˜˜˜                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:688:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                start_end.read_end.push_back(suffix[suffix_idx].second - good_it->d);  
                                             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:691:73: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                start_end.read_start.push_back(suffix[suffix_idx].second - good_it->d + 1);
                ˜˜˜˜˜˜˜˜˜                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
SpliceMap_utils_QuasR.cpp:691:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                start_end.read_start.push_back(suffix[suffix_idx].second - good_it->d + 1);
                                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:726:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                read_start_pos = suffix[suffix_idx].first;
                                                 ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:732:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                read_back_pos = suffix[suffix_idx].second;
                                                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:740:60: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                                start_end.read_end.push_back(suffix[suffix_idx].second - good_it->d);  
                                ˜˜˜˜˜˜˜˜˜                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:740:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                start_end.read_end.push_back(suffix[suffix_idx].second - good_it->d);  
                                                             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:743:75: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                                start_end.read_start.push_back(suffix[suffix_idx].second - good_it->d + 1);
                                ˜˜˜˜˜˜˜˜˜                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
SpliceMap_utils_QuasR.cpp:743:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                start_end.read_start.push_back(suffix[suffix_idx].second - good_it->d + 1);
                                                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:767:71: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                        start_end.read_end.push_back(suffix[suffix_idx].first + good_it->d - 1);
                        ˜˜˜˜˜˜˜˜˜                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
SpliceMap_utils_QuasR.cpp:767:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        start_end.read_end.push_back(suffix[suffix_idx].first + good_it->d - 1);
                                                     ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:769:52: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                        start_end.read_end.push_back(suffix[suffix_idx].second); 
                        ˜˜˜˜˜˜˜˜˜                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:769:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        start_end.read_end.push_back(suffix[suffix_idx].second); 
                                                     ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:775:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        read_start_pos = suffix[suffix_idx].first;
                                         ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:779:51: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                start_end.read_end.push_back(suffix[suffix_idx].second);
                ˜˜˜˜˜˜˜˜˜                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:779:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                start_end.read_end.push_back(suffix[suffix_idx].second);
                                             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:785:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        read_start_pos = suffix[suffix_idx].first;
                                         ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:795:59: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                        start_end.read_end.push_back(suffix[suffix_idx].second - good_it->d);  
                        ˜˜˜˜˜˜˜˜˜                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:795:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        start_end.read_end.push_back(suffix[suffix_idx].second - good_it->d);  
                                                     ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:798:74: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                        start_end.read_start.push_back(suffix[suffix_idx].second - good_it->d + 1);
                        ˜˜˜˜˜˜˜˜˜                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
SpliceMap_utils_QuasR.cpp:798:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        start_end.read_start.push_back(suffix[suffix_idx].second - good_it->d + 1);
                                                       ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:802:51: warning: implicit conversion loses integer precision: 'int' to 'const value_type' (aka 'const short') [-Wconversion]
                start_end.read_end.push_back(suffix[suffix_idx].second);  
                ˜˜˜˜˜˜˜˜˜                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:802:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                start_end.read_end.push_back(suffix[suffix_idx].second);  
                                             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:810:34: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
                start_end.read_start.front() = read_start_pos;
                                             ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
SpliceMap_utils_QuasR.cpp:816:31: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
                start_end.read_end.back() = read_back_pos;
                                          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
40 warnings generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
runSpliceMap_QuasR.cpp:108:31: warning: unused variable 'chr_file_list_it' [-Wunused-variable]
            vector<string>::iterator chr_file_list_it = chr_file_list.begin();
                                     ^
runSpliceMap_QuasR.cpp:190:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
            head_clip_length = atoi(temp.c_str());
                             ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:191:27: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
            if (head_clip_length < 0) {
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜
runSpliceMap_QuasR.cpp:197:31: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
            if (fullread_length>0 && fullread_length-head_clip_length < 50) {
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:443:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
            cout << "At most " << (fullread_length-head_clip_length) <<  " bases in total." << endl;
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:445:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
            debug_out << "At most " << (fullread_length-head_clip_length) <<  " bases in total." << endl;
                                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:539:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                    line = line.substr(head_clip_length, fullread_length-head_clip_length);   
                                                                         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:597:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                    line = line.substr(head_clip_length, fullread_length-head_clip_length);   
                                                                         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:663:56: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                    string new_filename = temp_path+"read_"+IntToStr(read_count)+"_"+IntToStr(k+1);
                                                            ˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:718:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                    line = line.substr(head_clip_length, fullread_length-head_clip_length);   
                                                                         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:809:56: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                    string new_filename = temp_path+"read_"+IntToStr(read_count)+"_"+IntToStr(k+1);
                                                            ˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:843:42: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                line = line.substr(head_clip_length, fullread_length-head_clip_length);   
                                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:1163:47: warning: implicit conversion loses integer precision: 'int' to 'int8_t' (aka 'signed char') [-Wconversion]
                                        contents.mismatch_dir = curr_num_mismatch*direction;
                                                              ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:1164:26: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        contents.location = chr_pos;
                                                          ˜ ^˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:1353:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    tabloc2 = (int) line.find('\t',tabloc+1);
                    ˜˜˜˜           ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1354:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    curr_flag = atoi(line.substr(tabloc+1, tabloc2-tabloc-1).c_str());
              ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:1354:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    curr_flag = atoi(line.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                     ˜˜˜˜        ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1354:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    curr_flag = atoi(line.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                     ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1356:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    curr_read_idx = atoi(line.substr(0,tabloc).c_str()) + 1;  
                         ˜˜˜˜          ^˜˜˜˜˜
runSpliceMap_QuasR.cpp:1380:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        tabloc2 = (int) line.find('\t',tabloc+1);
                        ˜˜˜˜           ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1381:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        curr_flag = atoi(line.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:1381:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        curr_flag = atoi(line.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                         ˜˜˜˜        ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1381:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        curr_flag = atoi(line.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                         ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1382:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int temp_curr_read_idx = atoi(line.substr(0,tabloc).c_str()) + 1;
                                      ˜˜˜˜          ^˜˜˜˜˜
runSpliceMap_QuasR.cpp:1403:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    tabloc2 = (int) temp.find('\t',tabloc+1); 
                                    ˜˜˜˜           ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1405:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    int temp_curr_flag = atoi(temp.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                                              ˜˜˜˜        ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1405:69: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    int temp_curr_flag = atoi(temp.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                                              ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1408:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    tabloc2 = (int) temp.find('\t',tabloc+1); 
                                    ˜˜˜˜           ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1410:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    curr_chr_name = temp.substr(tabloc+1, tabloc2-tabloc-1).c_str();
                                    ˜˜˜˜        ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1410:59: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    curr_chr_name = temp.substr(tabloc+1, tabloc2-tabloc-1).c_str();
                                    ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1413:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    tabloc2 = (int) temp.find('\t',tabloc+1); 
                                    ˜˜˜˜           ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1415:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    curr_pos = atoi(temp.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                                    ˜˜˜˜        ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1415:59: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    curr_pos = atoi(temp.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                                    ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1421:77: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                               << curr_chr_name << "\t" << curr_pos << "\t" << sam_get_direction(temp_curr_flag) << endl;
                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:1424:77: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                               << curr_chr_name << "\t" << curr_pos << "\t" << sam_get_direction(temp_curr_flag) << endl;
                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:1438:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        tabloc2 = (int) line.find('\t',tabloc+1);
                        ˜˜˜˜           ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1440:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        curr_read_idx = atoi(line.substr(0,tabloc).c_str()) + 1;
                             ˜˜˜˜          ^˜˜˜˜˜
runSpliceMap_QuasR.cpp:1472:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            tabloc2 = (int) temp.find('\t',tabloc+1); 
                            ˜˜˜˜           ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1474:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            int temp_curr_flag = atoi(temp.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                                      ˜˜˜˜        ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1474:68: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            int temp_curr_flag = atoi(temp.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                                      ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1477:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            tabloc2 = (int) temp.find('\t',tabloc+1); 
                            ˜˜˜˜           ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1479:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            curr_chr_name = temp.substr(tabloc+1, tabloc2-tabloc-1).c_str();
                            ˜˜˜˜        ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1479:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            curr_chr_name = temp.substr(tabloc+1, tabloc2-tabloc-1).c_str();
                            ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1482:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            tabloc2 = (int) temp.find('\t',tabloc+1); 
                            ˜˜˜˜           ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1484:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            curr_pos = atoi(temp.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                            ˜˜˜˜        ˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1484:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            curr_pos = atoi(temp.substr(tabloc+1, tabloc2-tabloc-1).c_str());
                            ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
runSpliceMap_QuasR.cpp:1490:76: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                       << curr_chr_name << "\t" << curr_pos << "\t" << sam_get_direction(temp_curr_flag) << endl;
                                                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:1493:76: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                       << curr_chr_name << "\t" << curr_pos << "\t" << sam_get_direction(temp_curr_flag) << endl;
                                                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
runSpliceMap_QuasR.cpp:1565:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            map_out << line.substr(it->first - 1,25) << '\n';    
                       ˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜^˜˜
runSpliceMap_QuasR.cpp:1566:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            map_out << line.substr(it->first+25 - 1,25) << '\n'; 
                       ˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
50 warnings generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
sortsam.cpp:98:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                tabloc = (int) line.find('\t',tabloc+1); 
                               ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:99:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                tabloc2 = (int) line.find('\t',tabloc+1); 
                                ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:100:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                chr_name = line.substr(tabloc+1, tabloc2 - tabloc - 1);
                           ˜˜˜˜        ˜˜˜˜˜˜^˜
sortsam.cpp:100:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                chr_name = line.substr(tabloc+1, tabloc2 - tabloc - 1);
                           ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
sortsam.cpp:105:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                tabloc2 = (int) line.find('\t',tabloc+1); 
                                ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:106:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                curr_pos = (uint_fast32_t)atoi(line.substr(tabloc+1, tabloc2 - tabloc - 1).c_str());
                                               ˜˜˜˜        ˜˜˜˜˜˜^˜
sortsam.cpp:106:73: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                curr_pos = (uint_fast32_t)atoi(line.substr(tabloc+1, tabloc2 - tabloc - 1).c_str());
                                               ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
sortsam.cpp:119:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        tabloc = (int) line.find('\t',tabloc+1); 
                                       ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:120:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        tabloc2 = (int) line.find('\t',tabloc+1); 
                                        ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:121:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        string temp_chr_name = line.substr(tabloc+1, tabloc2 - tabloc - 1);
                                               ˜˜˜˜        ˜˜˜˜˜˜^˜
sortsam.cpp:121:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        string temp_chr_name = line.substr(tabloc+1, tabloc2 - tabloc - 1);
                                               ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
sortsam.cpp:123:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        tabloc2 = (int) line.find('\t',tabloc+1); 
                                        ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:124:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        curr_pos = (uint_fast32_t)atoi(line.substr(tabloc+1, tabloc2 - tabloc - 1).c_str());
                                                       ˜˜˜˜        ˜˜˜˜˜˜^˜
sortsam.cpp:124:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        curr_pos = (uint_fast32_t)atoi(line.substr(tabloc+1, tabloc2 - tabloc - 1).c_str());
                                                       ˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
sortsam.cpp:170:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                curr_idx = atoi(line.substr(0,tabloc).c_str());
                                ˜˜˜˜          ^˜˜˜˜˜
sortsam.cpp:176:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                tabloc2 = (int) line.find('\t',tabloc+1); 
                                ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:178:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                tabloc2 = (int) line.find('\t',tabloc+1); 
                                ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:180:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                tabloc2 = (int) line.find('\t',tabloc+1); 
                                ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:183:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                line = line.substr(0,tabloc2) + "\t" +line.substr(line.length()-1);
                       ˜˜˜˜          ^˜˜˜˜˜˜
sortsam.cpp:186:19: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                temp_data.pos = curr_idx;
                              ˜ ^˜˜˜˜˜˜˜
sortsam.cpp:201:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        temp_curr_idx = atoi(line.substr(0,tabloc).c_str());
                                             ˜˜˜˜          ^˜˜˜˜˜
sortsam.cpp:205:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        tabloc2 = (int) line.find('\t',tabloc+1); 
                                        ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:207:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        tabloc2 = (int) line.find('\t',tabloc+1); 
                                        ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:209:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        tabloc2 = (int) line.find('\t',tabloc+1); 
                                        ˜˜˜˜           ˜˜˜˜˜˜^˜
sortsam.cpp:212:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        line = line.substr(0,tabloc2) + "\t" +line.substr(line.length()-1);
                               ˜˜˜˜          ^˜˜˜˜˜˜
sortsam.cpp:215:21: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                temp_data.pos = curr_idx;
                                              ˜ ^˜˜˜˜˜˜˜
sortsam.cpp:220:38: warning: implicit conversion changes signedness: 'const uint_fast32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                                int top_index = data_queue.top().pos; 
                                    ˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
sortsam.cpp:233:36: warning: implicit conversion changes signedness: 'const uint_fast32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
                                                top_index = data_queue.top().pos;
                                                          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
sortsam.cpp:244:22: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        temp_data.pos = curr_idx;
                                                      ˜ ^˜˜˜˜˜˜˜
sortsam.cpp:251:22: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        temp_data.pos = curr_idx;
                                                      ˜ ^˜˜˜˜˜˜˜
30 warnings generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
amalgamateSAM.cpp:18:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    end_pos = buffer.find(']', start_pos);
              ˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:19:18: warning: comparison of constant 18446744073709551615 with expression of type 'int' is always true [-Wtautological-constant-out-of-range-compare]
    if(start_pos != string::npos && end_pos != string::npos)
       ˜˜˜˜˜˜˜˜˜ ^  ˜˜˜˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:19:45: warning: comparison of constant 18446744073709551615 with expression of type 'int' is always true [-Wtautological-constant-out-of-range-compare]
    if(start_pos != string::npos && end_pos != string::npos)
                                    ˜˜˜˜˜˜˜ ^  ˜˜˜˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:20:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return atoi(buffer.substr(start_pos, end_pos-start_pos).c_str());
                    ˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:20:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return atoi(buffer.substr(start_pos, end_pos-start_pos).c_str());
                    ˜˜˜˜˜˜                   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:17:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    start_pos = buffer.find('[')+1;
              ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
amalgamateSAM.cpp:18:15: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    end_pos = buffer.find(']', start_pos);
            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:390:40: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
                                    random_read_select[0] = rand() % curr_read_group.size();
                                                          ˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:390:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                    random_read_select[0] = rand() % curr_read_group.size();
                                                            ^˜˜˜˜˜ ˜
amalgamateSAM.cpp:391:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                    tmp_line_str = curr_read_group[random_read_select[0]].data;
                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:510:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                (*(outsam_list[curr_read_group_it->file_index])) << line_str << '\n';
                                                   ˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:544:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        (*(outsam_list[curr_read_group_it->file_index])) << line_str << '\n';
                                           ˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:701:29: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                uint_fast32_t start_loc = atoi(line_list[3].c_str());
                              ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:772:73: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'const key_type' (aka 'const int') [-Wsign-conversion]
                                jundict_ij_t::iterator jun_it = ((jundict_pair.first)->second).find(chr_pos);
                                                                ˜                                   ^˜˜˜˜˜˜
amalgamateSAM.cpp:775:64: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'const key_type' (aka 'const int') [-Wsign-conversion]
                                        jundict_b_ij_t::iterator jun_b_it = (jun_it->second).find(right_start);
                                                                            ˜                     ^˜˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:806:54: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                                                (jun_it->second).insert(pair<int,jun_store_ij>(right_start,store));
                                                                        ˜˜˜˜                   ^˜˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:826:46: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                                        jundict_b.insert(pair<int,jun_store_ij>(right_start,store));
                                                         ˜˜˜˜                   ^˜˜˜˜˜˜˜˜˜˜
amalgamateSAM.cpp:827:69: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                                        ((jundict_pair.first)->second).insert(pair<int,jundict_b_ij_t>(chr_pos,jundict_b));
                                                                              ˜˜˜˜                     ^˜˜˜˜˜˜
18 warnings generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
getSpliceMapUnmapped.cpp:73:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            newid = atoi(buffer.substr(start_pos, end_pos-start_pos).c_str());
                         ˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜
getSpliceMapUnmapped.cpp:73:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            newid = atoi(buffer.substr(start_pos, end_pos-start_pos).c_str());
                         ˜˜˜˜˜˜                   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
getSpliceMapUnmapped.cpp:71:35: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
            start_pos = buffer.rfind('[')+1;
                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
getSpliceMapUnmapped.cpp:72:16: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            end_pos = buffer.rfind(']');
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getSpliceMapUnmapped.cpp:88:18: warning: comparison of constant 18446744073709551615 with expression of type 'int' is always true [-Wtautological-constant-out-of-range-compare]
    if(start_pos != string::npos && end_pos != string::npos)
       ˜˜˜˜˜˜˜˜˜ ^  ˜˜˜˜˜˜˜˜˜˜˜˜
getSpliceMapUnmapped.cpp:88:45: warning: comparison of constant 18446744073709551615 with expression of type 'int' is always true [-Wtautological-constant-out-of-range-compare]
    if(start_pos != string::npos && end_pos != string::npos)
                                    ˜˜˜˜˜˜˜ ^  ˜˜˜˜˜˜˜˜˜˜˜˜
getSpliceMapUnmapped.cpp:89:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return atoi(buffer.substr(start_pos, end_pos-start_pos).c_str());
                    ˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜
getSpliceMapUnmapped.cpp:89:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return atoi(buffer.substr(start_pos, end_pos-start_pos).c_str());
                    ˜˜˜˜˜˜                   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
getSpliceMapUnmapped.cpp:86:34: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    start_pos = buffer.rfind('[')+1;
              ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
getSpliceMapUnmapped.cpp:87:15: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    end_pos = buffer.rfind(']');
            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getSpliceMapUnmapped.cpp:188:15: warning: variable 'nbIn' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
    } else if(argv[1][0] == 'P') { // paired-end mode
              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getSpliceMapUnmapped.cpp:300:16: note: uninitialized use occurs here
    for(i=0; i<nbIn; i++)
               ^˜˜˜
getSpliceMapUnmapped.cpp:188:12: note: remove the 'if' if its condition is always true
    } else if(argv[1][0] == 'P') { // paired-end mode
           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getSpliceMapUnmapped.cpp:107:20: note: initialize the variable 'nbIn' to silence this warning
    int i, id, nbIn;
                   ^
                    = 0
11 warnings generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
fuseReorder.cpp:218:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for(i=0; i<nbChr; i++) cout << chrName[i] << '\t' << chrPos[i] << endl;
                                   ˜˜˜˜˜˜˜ ^
fuseReorder.cpp:218:65: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for(i=0; i<nbChr; i++) cout << chrName[i] << '\t' << chrPos[i] << endl;
                                                         ˜˜˜˜˜˜ ^
fuseReorder.cpp:222:22: warning: variable length arrays are a C99 feature [-Wvla]
    samFile *samfiles[nbChr+2];
                     ^
fuseReorder.cpp:224:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        samfiles[i] = new samFile(fnameIn[0], chrPos[i], i<nbChr-1 ? chrPos[i+1] : (streampos)0, i); // junction.sam (chromosome blocks)
                                              ˜˜˜˜˜˜ ^
fuseReorder.cpp:224:71: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        samfiles[i] = new samFile(fnameIn[0], chrPos[i], i<nbChr-1 ? chrPos[i+1] : (streampos)0, i); // junction.sam (chromosome blocks)
                                                                     ˜˜˜˜˜˜ ˜^˜
5 warnings generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
main.cpp:223:22: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                        intron_curve[0] = min_intron;
                                        ˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:225:22: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                        intron_curve[2] = max_intron;
                                        ˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:229:22: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                        intron_curve[2] = max_intron;
                                        ˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:231:22: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                        intron_curve[0] = min_intron;
                                        ˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:232:32: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                        intron_curve[1] = max_intron*5;
                                        ˜ ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:233:32: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                        intron_curve[2] = min_intron*20;
                                        ˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
main.cpp:240:20: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                min_extend_req = atoi(temp.c_str()); 
                               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:319:30: warning: implicit conversion changes signedness: 'uint_fast64_t' (aka 'unsigned long long') to 'streamoff' (aka 'long long') [-Wsign-conversion]
                genome_filename_file.seekg(genome_file_index_start); 
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:373:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        key_num = key_num + (val<<(2*num_read));
                                          ˜  ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:382:15: warning: implicit conversion changes signedness: 'int' to 'const value_type' (aka 'const unsigned int') [-Wsign-conversion]
        v->push_back(pos);
        ˜            ^˜˜
main.cpp:395:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        key_num = key_num + (val<<18);  
                                          ˜  ˜˜˜^˜˜˜
main.cpp:411:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        key_num = key_num + (val<<(2*num_read));
                                                          ˜  ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:429:35: warning: implicit conversion changes signedness: 'int' to 'const value_type' (aka 'const unsigned int') [-Wsign-conversion]
                        chrdict_10[key_num]->push_back(pos);
                        ˜˜˜˜˜˜˜˜˜˜                     ^˜˜
main.cpp:432:19: warning: implicit conversion changes signedness: 'int' to 'const value_type' (aka 'const unsigned int') [-Wsign-conversion]
                        vec->push_back(pos);
                        ˜˜˜            ^˜˜
main.cpp:572:25: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                        fullread_length[0] = atoi(line.c_str());
                                           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:582:26: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                fullread_length[1] = atoi(line.c_str());
                                                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:590:42: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                suffix_list[pair_idx] = designsuffix(fullread_length[pair_idx]);
                                                        ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:633:63: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        uint_fast32_t local_start = (suffix_list[pair_idx][seg]).first;
                                                      ˜˜˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:634:61: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        uint_fast32_t local_end = (suffix_list[pair_idx][seg]).second;
                                                      ˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:724:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                m.seed_line = linefullreads.substr(k * read_halflen, read_halflen);
                                                                              ˜˜˜˜˜˜˜˜˜˜˜˜˜        ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:724:62: warning: implicit conversion changes signedness: 'const int_fast32_t' (aka 'const int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                m.seed_line = linefullreads.substr(k * read_halflen, read_halflen);
                                                                              ˜˜˜˜˜˜˜˜˜˜˜˜˜                          ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:784:66: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                        uint_fast32_t chr_pos = mix_temp_line.coor - 1 + ((k+1)%2)*(read_halflen-1); 
                                                                                                       ˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:797:67: warning: implicit conversion changes signedness: 'const int_fast32_t' (aka 'const int') to 'unsigned int' [-Wsign-conversion]
                                                                while (read_pos < 50 && chr_pos < (uint_fast32_t)(chrsize-read_halflen) 
                                                                                                                         ˜^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:798:40: warning: implicit conversion changes signedness: 'int_fast32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                           && mix_temp_line.full_line[read_pos] == chrline[chr_pos]) {  
                                                                              ˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜
main.cpp:806:53: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                                                                                        coord_list[0].push_back(coord_t(read_pos,chr_pos));
                                                                                                                ˜˜˜˜˜˜˜          ^˜˜˜˜˜˜
main.cpp:809:53: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                                                                                        coord_list[1].push_back(coord_t(read_pos,chr_pos));
                                                                                                                ˜˜˜˜˜˜˜          ^˜˜˜˜˜˜
main.cpp:813:52: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                                                                                coord_list[0].push_back(coord_t(read_pos,chr_pos));
                                                                                                        ˜˜˜˜˜˜˜          ^˜˜˜˜˜˜
main.cpp:830:102: warning: implicit conversion changes signedness: 'int_fast32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                while (read_pos >= 0 && chr_pos > (uint_fast32_t)(read_halflen-1) && mix_temp_line.full_line[read_pos] == chrline[chr_pos]) {
                                                                                                                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜
main.cpp:842:53: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                                                                                        coord_list[0].push_back(coord_t(read_pos,chr_pos));
                                                                                                                ˜˜˜˜˜˜˜          ^˜˜˜˜˜˜
main.cpp:845:53: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                                                                                        coord_list[1].push_back(coord_t(read_pos,chr_pos));
                                                                                                                ˜˜˜˜˜˜˜          ^˜˜˜˜˜˜
main.cpp:848:52: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'const int' [-Wsign-conversion]
                                                                                coord_list[1].push_back(coord_t(read_pos,chr_pos));
                                                                                                        ˜˜˜˜˜˜˜          ^˜˜˜˜˜˜
main.cpp:857:43: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                                        int furthest_read_extend_chr_pos = chr_pos;
                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜
main.cpp:876:24: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                                        chr_pos = it->second; 
                                                                                ˜ ˜˜˜˜^˜˜˜˜˜
main.cpp:880:61: warning: implicit conversion changes signedness: 'int_fast32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                string line_left = mix_temp_line.full_line.substr(read_pos); 
                                                                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜˜˜
main.cpp:891:61: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                                                                uint_fast32_t half_distance = cal_half_distance(line_left_len,intron_curve);
                                                                                                                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:893:167: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                                                                pair<vector<uint_fast32_t>::iterator, vector<uint_fast32_t>::iterator> left_indexlist = checkindexlistFwd(chr_pos, (*chrdict_10[key_val]), half_distance, min_intron_search_distance);
                                                                                                                                                                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:899:62: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                                                        if (DNA_mode && *index_it == chr_pos - (read_pos-8)) {
                                                                                                                                             ˜  ˜˜˜˜˜˜˜˜^˜
main.cpp:908:56: warning: implicit conversion changes signedness: 'const int_fast32_t' (aka 'const int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                                tempread = chrline.substr((*index_it)-1, read_halflen);  
                                                                                                                           ˜˜˜˜˜˜˜                       ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:924:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                                while (i < line_left_len && tempread[i] == line_left[i]) { 
                                                                                                                                            ˜˜˜˜˜˜˜˜ ^
main.cpp:924:68: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                                while (i < line_left_len && tempread[i] == line_left[i]) { 
                                                                                                                                                           ˜˜˜˜˜˜˜˜˜ ^
main.cpp:934:29: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int_fast32_t' (aka 'int') [-Wsign-conversion]
                                                                                                                        contents.a = chr_pos;
                                                                                                                                   ˜ ^˜˜˜˜˜˜
main.cpp:935:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int_fast32_t' (aka 'int') [-Wsign-conversion]
                                                                                                                        contents.b = (*index_it);
                                                                                                                                   ˜  ^˜˜˜˜˜˜˜˜
main.cpp:950:72: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                string line_left = mix_temp_line.full_line.substr(0, read_pos+1);
                                                                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜                     ˜˜˜˜˜˜˜˜^˜
main.cpp:955:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                        string line_left_10 = line_left.substr(line_left_len-10, 10);
                                                                                                              ˜˜˜˜˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
main.cpp:962:61: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                                                                uint_fast32_t half_distance = cal_half_distance(line_left_len,intron_curve);
                                                                                                                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:964:167: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
                                                                                                pair<vector<uint_fast32_t>::iterator, vector<uint_fast32_t>::iterator> left_indexlist = checkindexlistRes(chr_pos, (*chrdict_10[key_val]), half_distance, min_intron_search_distance);
                                                                                                                                                                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:969:62: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                                                        if (DNA_mode && *index_it == chr_pos - (read_pos-10)) {
                                                                                                                                             ˜  ˜˜˜˜˜˜˜˜^˜˜
main.cpp:979:53: warning: implicit conversion changes signedness: 'const int_fast32_t' (aka 'const int') to 'unsigned int' [-Wsign-conversion]
                                                                                                                tempread = chrline.substr((*index_it)-read_halflen+9, read_halflen); 
                                                                                                                                                     ˜^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:979:69: warning: implicit conversion changes signedness: 'const int_fast32_t' (aka 'const int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                                tempread = chrline.substr((*index_it)-read_halflen+9, read_halflen); 
                                                                                                                           ˜˜˜˜˜˜˜                                    ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:995:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                                while (i < line_left_len && tempread[read_halflen-i-1] == line_left[line_left_len-i-1]) { 
                                                                                                                                            ˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:995:98: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                                while (i < line_left_len && tempread[read_halflen-i-1] == line_left[line_left_len-i-1]) { 
                                                                                                                                                                          ˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:1001:29: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int_fast32_t' (aka 'int') [-Wsign-conversion]
                                                                                                                        contents.a = chr_pos;
                                                                                                                                   ˜ ^˜˜˜˜˜˜
main.cpp:1002:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int_fast32_t' (aka 'int') [-Wsign-conversion]
                                                                                                                        contents.b = (*index_it);
                                                                                                                                   ˜  ^˜˜˜˜˜˜˜˜
main.cpp:1387:73: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                                        while (temp_group.size() == 0 && (singleread_group_result.size()-num_pop) >= 2) {
                                                                                                                        ˜^˜˜˜˜˜˜
main.cpp:1428:82: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                                                        vector<coord_t>::iterator suffix_end_it = seg_suffix_list.first.begin() + temp_group.front().size();
                                                                                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1433:57: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                                                        suffix_end_it = seg_suffix_list.second.begin() + temp_group.front().size();
                                                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1775:68: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                                pair<pair<int,int>,string> cigar = roll_cigar(curr_start_end,fullread_length[0],cufflinks);
                                                                                   ˜˜˜˜˜˜˜˜˜˜                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1784:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        read_out = full_line_read[0].substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second) + "\t";   
                                                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:1784:98: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out = full_line_read[0].substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second) + "\t";   
                                                                                                                                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:1784:118: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out = full_line_read[0].substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second) + "\t";   
                                                                                                                                                                      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:1797:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        read_out = temp.substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second) + "\t"; 
                                                                                   ˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:1797:85: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out = temp.substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second) + "\t"; 
                                                                                                                                     ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:1797:105: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out = temp.substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second) + "\t"; 
                                                                                                                                                         ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:1850:77: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[0],'I').substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second) ;
                                                                                         ˜˜˜˜˜˜                                ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:1850:117: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[0],'I').substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second) ;
                                                                                                                                                                     ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:1850:137: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[0],'I').substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second) ;
                                                                                                                                                                                         ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:1857:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[0].substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second);   
                                                                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:1857:104: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[0].substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second);   
                                                                                                                                                        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:1857:124: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[0].substr(cigar.first.first, fullread_length[0] - cigar.first.first - cigar.first.second);   
                                                                                                                                                                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:1929:76: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                                        if (checkPairInfo(*(side_seg_jun_list[0]), *(side_seg_jun_list[1]), intron_curve[2])) {
                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜                                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2122:48: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                                        cigar[0] = roll_cigar(curr_start_end[0],fullread_length[0],cufflinks);
                                                                   ˜˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2123:48: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                                        cigar[1] = roll_cigar(curr_start_end[1],fullread_length[1],cufflinks);
                                                                   ˜˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2136:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        read_out[0] = full_line_read[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t";   
                                                                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2136:107: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[0] = full_line_read[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t";   
                                                                                                                                                        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2136:130: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[0] = full_line_read[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t";   
                                                                                                                                                                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2137:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        read_out[1] = temp.substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) + "\t";   
                                                                                      ˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2137:94: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[1] = temp.substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) + "\t";   
                                                                                                                                           ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2137:117: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[1] = temp.substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) + "\t";   
                                                                                                                                                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2151:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        read_out[0] = temp.substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t"; 
                                                                                      ˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2151:94: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[0] = temp.substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t"; 
                                                                                                                                           ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2151:117: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[0] = temp.substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t"; 
                                                                                                                                                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2152:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        read_out[1] = full_line_read[1].substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) + "\t"; 
                                                                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2152:107: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[1] = full_line_read[1].substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) + "\t"; 
                                                                                                                                                        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2152:130: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[1] = full_line_read[1].substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) + "\t"; 
                                                                                                                                                                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2175:48: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                                        cigar[0] = roll_cigar(curr_start_end[0],fullread_length[0],cufflinks);
                                                                   ˜˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2183:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        read_out[0] = full_line_read[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t";   
                                                                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2183:107: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[0] = full_line_read[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t";   
                                                                                                                                                        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2183:130: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[0] = full_line_read[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t";   
                                                                                                                                                                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2194:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        read_out[0] = temp.substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t"; 
                                                                                      ˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2194:94: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[0] = temp.substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t"; 
                                                                                                                                           ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2194:117: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[0] = temp.substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) + "\t"; 
                                                                                                                                                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2217:48: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                                        cigar[1] = roll_cigar(curr_start_end[1],fullread_length[1],cufflinks);
                                                                   ˜˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2226:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        read_out[1] = full_line_read[1].substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) + "\t";   
                                                                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2226:107: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[1] = full_line_read[1].substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) + "\t";   
                                                                                                                                                        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2226:130: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[1] = full_line_read[1].substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) + "\t";   
                                                                                                                                                                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2237:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        read_out[1] = temp.substr(cigar[1].first.first, fullread_length[1]  - cigar[1].first.first - cigar[1].first.second) + "\t"; 
                                                                                      ˜˜˜˜        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2237:95: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[1] = temp.substr(cigar[1].first.first, fullread_length[1]  - cigar[1].first.first - cigar[1].first.second) + "\t"; 
                                                                                                                                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2237:118: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        read_out[1] = temp.substr(cigar[1].first.first, fullread_length[1]  - cigar[1].first.first - cigar[1].first.second) + "\t"; 
                                                                                                                                                                   ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2306:80: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[0],'I').substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) ;
                                                                                         ˜˜˜˜˜˜                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2306:123: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[0],'I').substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) ;
                                                                                                                                                                        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2306:146: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[0],'I').substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) ;
                                                                                                                                                                                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2313:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second);   
                                                                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2313:110: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second);   
                                                                                                                                                           ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2313:133: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second);   
                                                                                                                                                                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2396:80: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[1],'I').substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) ;
                                                                                         ˜˜˜˜˜˜                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2396:123: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[1],'I').substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) ;
                                                                                                                                                                        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2396:146: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[1],'I').substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second) ;
                                                                                                                                                                                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2403:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[1].substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second);   
                                                                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2403:110: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[1].substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second);   
                                                                                                                                                           ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2403:133: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[1].substr(cigar[1].first.first, fullread_length[1] - cigar[1].first.first - cigar[1].first.second);   
                                                                                                                                                                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2483:80: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[0],'I').substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) ;
                                                                                         ˜˜˜˜˜˜                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2483:123: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[0],'I').substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) ;
                                                                                                                                                                        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2483:146: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[0],'I').substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second) ;
                                                                                                                                                                                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2490:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second);   
                                                                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2490:110: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second);   
                                                                                                                                                           ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2490:133: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[0].substr(cigar[0].first.first, fullread_length[0] - cigar[0].first.first - cigar[0].first.second);   
                                                                                                                                                                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2567:80: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[1],'I').substr(cigar[1].first.first, fullread_length[1]  - cigar[1].first.first - cigar[1].first.second) ;
                                                                                         ˜˜˜˜˜˜                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2567:124: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[1],'I').substr(cigar[1].first.first, fullread_length[1]  - cigar[1].first.first - cigar[1].first.second) ;
                                                                                                                                                                         ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2567:147: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << string(fullread_length[1],'I').substr(cigar[1].first.first, fullread_length[1]  - cigar[1].first.first - cigar[1].first.second) ;
                                                                                                                                                                                                ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2574:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[1].substr(cigar[1].first.first, fullread_length[1]  - cigar[1].first.first - cigar[1].first.second);   
                                                                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2574:111: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[1].substr(cigar[1].first.first, fullread_length[1]  - cigar[1].first.first - cigar[1].first.second);   
                                                                                                                                                            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:2574:134: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                                        good_SAM_file << full_line_qual[1].substr(cigar[1].first.first, fullread_length[1]  - cigar[1].first.first - cigar[1].first.second);   
                                                                                                                                                                                   ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
main.cpp:2802:15: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
        int result = intron_curve[0];
            ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2804:12: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                result = intron_curve[0];
                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2806:12: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                result = intron_curve[1];
                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2808:12: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                result = intron_curve[2];
                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2811:9: warning: implicit conversion changes signedness: 'int' to 'uint_fast32_t' (aka 'unsigned int') [-Wsign-conversion]
        return result;
        ˜˜˜˜˜˜ ^˜˜˜˜˜
main.cpp:2826:19: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                int pos1 = it1->coor;
                    ˜˜˜˜   ˜˜˜˜˜^˜˜˜
main.cpp:2829:20: warning: implicit conversion changes signedness: 'uint_fast32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        int pos2 = it2->coor;
                            ˜˜˜˜   ˜˜˜˜˜^˜˜˜
main.cpp:2971:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                int val = get_base_val(s[i]);
                                       ˜ ^
main.cpp:3009:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        int len_list = (int)singleread_group_result[ref_group_index].size();
                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3020:69: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        for (vector<good_t>::iterator junction = singleread_group_result[ref_group_index].begin()
                                                                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3021:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                 ; junction != singleread_group_result[ref_group_index].end(); junction++) {
                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3032:84: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                check_overlap = check_segment_overlap(singleread_group_result[ref_group_index-1][ref_index->first],
                                                                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3032:99: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                check_overlap = check_segment_overlap(singleread_group_result[ref_group_index-1][ref_index->first],
                                                                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                    ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:3033:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                                           *junction, (range_list.first)[ref_group_index-1], (range_list.first)[ref_group_index]);
                                                                                                                                      ˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3033:88: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                                           *junction, (range_list.first)[ref_group_index-1], (range_list.first)[ref_group_index]);
                                                                                                                                                                             ˜                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3035:84: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                check_overlap = check_segment_overlap(singleread_group_result[ref_group_index-1][ref_index->first],
                                                                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3035:99: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                check_overlap = check_segment_overlap(singleread_group_result[ref_group_index-1][ref_index->first],
                                                                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                    ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:3036:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                                          *junction, (range_list.second)[ref_group_index], (range_list.second)[ref_group_index-1]);
                                                                                                                                     ˜                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3036:102: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                                          *junction, (range_list.second)[ref_group_index], (range_list.second)[ref_group_index-1]);
                                                                                                                                                                           ˜                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3076:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        one_output.push_back(singleread_group_result[ref_group_index][index->first]);
                                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3076:73: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        one_output.push_back(singleread_group_result[ref_group_index][index->first]);
                                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                  ˜˜˜˜˜˜˜^˜˜˜˜
main.cpp:3102:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                one_output.push_back(singleread_group_result[ref_group_index][good_index]);
                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3102:65: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                one_output.push_back(singleread_group_result[ref_group_index][good_index]);
                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜˜˜˜˜
main.cpp:3107:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                one_output.push_back(singleread_group_result[ref_group_index][good_index]);
                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3107:65: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                one_output.push_back(singleread_group_result[ref_group_index][good_index]);
                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜˜˜˜˜
main.cpp:3332:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if (read[r-1] != genome[c-1]) {
                            ˜˜˜˜ ˜^˜
main.cpp:3332:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if (read[r-1] != genome[c-1]) {
                                         ˜˜˜˜˜˜ ˜^˜
main.cpp:3334:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        MD_str += IntToStr(match_count) + genome[c-1];
                                                                          ˜˜˜˜˜˜ ˜^˜
main.cpp:3336:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        MD_str += genome[c-1];
                                                  ˜˜˜˜˜˜ ˜^˜
151 warnings generated.
MAKE of SpliceMap DONE
mkdir -p ../inst
cp SpliceMap/SpliceMap ../inst/SpliceMap
cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM
cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped
cp SpliceMap/fuseReorder ../inst/fuseReorder
cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR
cp SpliceMap/sortsam ../inst/sortsam
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rbowtie)

Rbowtie.Rcheck/Rbowtie-Ex.timings:

nameusersystemelapsed
Rbowtie-package0.0100.0020.012
Rbowtie7.5610.6648.561
SpliceMap3.7400.3925.561