>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rbowtie.buildbin-libdir Rbowtie_1.0.2.tar.gz'
>>>>>>>
* installing *source* package 'Rbowtie' ...
rm -f bowtie-build bowtie \
bowtie_prof \
bowtie-build.exe bowtie.exe bowtie_prof.exe \
bowtie-src.zip bowtie-bin.zip
rm -f core.*
rm -f SpliceMap/*.o SpliceMap/SpliceMap SpliceMap/amalgamateSAM SpliceMap/getSpliceMapUnmapped SpliceMap/fuseReorder SpliceMap/runSpliceMap_QuasR SpliceMap/sortsam
rm -f core.* ../inst/bowtie ../inst/bowtie-build ../inst/SpliceMap ../inst/amalgamateSAM ../inst/getSpliceMapUnmapped ../inst/fuseReorder ../inst/runSpliceMap_QuasR ../inst/sortsam
** libs
** arch -
clang++ -O3 -DCOMPILER_OPTIONS="\"-O3 -mtune=native -g -O2 -Wall -pedantic -Wconversion -mtune=native -g -O2 -Wall -pedantic -Wconversion\"" -mtune=native -g -O2 -Wall -pedantic -Wconversion -mtune=native -g -O2 -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 -g -O2 -Wall -pedantic -Wconversion -mtune=native -g -O2 -Wall -pedantic -Wconversion\"" -mtune=native -g -O2 -Wall -pedantic -Wconversion -mtune=native -g -O2 -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()
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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++) {
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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)