Package: bcSeq

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bcSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings bcSeq_1.2.0.tar.gz

StartedAt: 2018-10-17 00:38:56 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:41:15 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 138.3 seconds

RetCode: 0

Status:  OK

CheckDir: bcSeq.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bcSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings bcSeq_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/bcSeq.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bcSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bcSeq' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'bcSeq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/bcSeq/libs/i386/bcSeq.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test_bcSeq.R'
 OK
** running tests for arch 'x64' ...
  Running 'test_bcSeq.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/bcSeq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/bcSeq_1.2.0.tar.gz && rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bcSeq.buildbin-libdir bcSeq_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL bcSeq_1.2.0.zip && rm bcSeq_1.2.0.tar.gz bcSeq_1.2.0.zip
###
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100 22405  100 22405    0     0   412k      0 --:--:-- --:--:-- --:--:--  475k

install for i386

* installing *source* package 'bcSeq' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c CRISPR_matching.cpp -o CRISPR_matching.o
In file included from helper/count.h:5:0,
                 from CRISPR_matching.cpp:3:
helper/../structures/Trie.h: In member function 'bool state_t::end()':
helper/../structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   auto end() -> bool { return seqIdx == seq.size() - 1; }
                                      ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c Trie_edit.cpp -o Trie_edit.o
In file included from Trie_edit.cpp:1:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   auto end() -> bool { return seqIdx == seq.size() - 1; }
                                      ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c Trie_hamming.cpp -o Trie_hamming.o
In file included from Trie_hamming.cpp:1:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   auto end() -> bool { return seqIdx == seq.size() - 1; }
                                      ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c Trie_util.cpp -o Trie_util.o
In file included from Trie_util.cpp:2:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   auto end() -> bool { return seqIdx == seq.size() - 1; }
                                      ^
Trie_util.cpp: In member function 'bool Trie::setTMat(Rcpp::StringVector, Rcpp::NumericVector)':
Trie_util.cpp:105:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (MatSeq.length() != corLength) {
                           ^
In file included from structures/Trie.h:15:0,
                 from Trie_util.cpp:2:
structures/Node.h: In member function 'void Trie::addSeq(const string&, int)':
structures/Node.h:31:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
     int i;
         ^
structures/Node.h:53:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
     int i;
         ^
structures/Node.h:53:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c alignment.cpp -o alignment.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c trimRead.cpp -o trimRead.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c uniqueBar.cpp -o uniqueBar.o
uniqueBar.cpp: In function 'void uniqueBar(Rcpp::String, Rcpp::String)':
uniqueBar.cpp:21:9: warning: unused variable 'length' [-Wunused-variable]
     int length = 0;
         ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o bcSeq.dll tmp.def CRISPR_matching.o RcppExports.o Trie_edit.o Trie_hamming.o Trie_util.o alignment.o init.o trimRead.o uniqueBar.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/bcSeq.buildbin-libdir/bcSeq/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'bcSeq'
    finding HTML links ... done
    bcSeq-package                           html  
    finding level-2 HTML links ... done

    bcSeq_edit                              html  
    bcSeq_hamming                           html  
    trimRead                                html  
    uniqueBar                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'bcSeq' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c CRISPR_matching.cpp -o CRISPR_matching.o
In file included from helper/count.h:5:0,
                 from CRISPR_matching.cpp:3:
helper/../structures/Trie.h: In member function 'bool state_t::end()':
helper/../structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   auto end() -> bool { return seqIdx == seq.size() - 1; }
                                      ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c Trie_edit.cpp -o Trie_edit.o
In file included from Trie_edit.cpp:1:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   auto end() -> bool { return seqIdx == seq.size() - 1; }
                                      ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c Trie_hamming.cpp -o Trie_hamming.o
In file included from Trie_hamming.cpp:1:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   auto end() -> bool { return seqIdx == seq.size() - 1; }
                                      ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c Trie_util.cpp -o Trie_util.o
In file included from Trie_util.cpp:2:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   auto end() -> bool { return seqIdx == seq.size() - 1; }
                                      ^
Trie_util.cpp: In member function 'bool Trie::setTMat(Rcpp::StringVector, Rcpp::NumericVector)':
Trie_util.cpp:105:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (MatSeq.length() != corLength) {
                           ^
In file included from structures/Trie.h:15:0,
                 from Trie_util.cpp:2:
structures/Node.h: In member function 'void Trie::addSeq(const string&, int)':
structures/Node.h:31:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
     int i;
         ^
structures/Node.h:53:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
     int i;
         ^
structures/Node.h:53:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c alignment.cpp -o alignment.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c trimRead.cpp -o trimRead.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Matrix/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c uniqueBar.cpp -o uniqueBar.o
uniqueBar.cpp: In function 'void uniqueBar(Rcpp::String, Rcpp::String)':
uniqueBar.cpp:21:9: warning: unused variable 'length' [-Wunused-variable]
     int length = 0;
         ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o bcSeq.dll tmp.def CRISPR_matching.o RcppExports.o Trie_edit.o Trie_hamming.o Trie_util.o alignment.o init.o trimRead.o uniqueBar.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/bcSeq.buildbin-libdir/bcSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bcSeq' as bcSeq_1.2.0.zip
* DONE (bcSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'bcSeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(bcSeq)
> #devtools::load_all("../")
> #### Set the seed
> set.seed(4523)
> 
> #### Generate barcode
> lFName    <- "./libFile.fasta"
> bases     <- c(rep('A', 4), rep('C',4), rep('G',4), rep('T',4))
> numOfBars <- 7
> Barcodes  <- rep(NA, numOfBars*2)
> for (i in 1:numOfBars){
+     Barcodes[2*i-1] <- paste0(">barcode_ID: ", i)
+     Barcodes[2*i]   <- paste(sample(bases, length(bases)), collapse = '')
+ }
> write(Barcodes, lFName)
> 
> #### Generate reads and phred score
> rFName     <- "./readFile.fastq"
> numOfReads <- 8
> Reads      <- rep(NA, numOfReads*4)
> for (i in 1:numOfReads){
+     Reads[4*i-3] <- paste0("@read_ID_",i)
+     Reads[4*i-2] <- Barcodes[2*sample(1:numOfBars,1,
+                   replace=TRUE, prob=seq(1:numOfBars))]
+     Reads[4*i-1] <- "+"
+     Reads[4*i]   <- paste(rawToChar(as.raw(
+                   33+sample(20:30, length(bases),replace=TRUE))),
+                   collapse='')
+ }
> write(Reads, rFName)
> 
> #### perform alignment 
> ReadFile <- "./readFile.fastq"
> BarFile  <- "./libFile.fasta"
> outFile  <- "./countH.csv"
> 
> #### with default output for bcSeq_hamming
> res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
+     tMat = NULL, numThread = 2, count_only = TRUE )
Running hamming search with 4 sequences per thread in 2 threads
Compiling results
> res <- read.csv(outFile, header=FALSE)
> res
                V1 V2
1 TCCGACGCAAGTGATT  0
2 TATCGCTGAATGAGCC  0
3 AATCGGTGGCACATCT  2
4 GAGTCTCTGGATACAC  1
5 CGACAGTAATCGCTTG  2
6 ACCAGTAGTCAGGTTC  1
7 TAAGCAGGCGTCTTAC  2
> 
> #### with return of alignment probability matrix to R
> #outFile  <- "./countH2.csv"
> #res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
> #    tMat = NULL, numThread = 2, count_only = FALSE )
> #res 
> 
> #### with default output for bcSeq_edit
> outFile  <- "./countE.csv"
> res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
+     tMat = NULL, numThread = 2, count_only = TRUE,
+     gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
+     pen_max = 7)
Running levenshtein search with 4 sequences per thread in 2 threads
Compiling results
> res <- read.csv(outFile, header=FALSE)
> res
                V1 V2
1 TCCGACGCAAGTGATT  0
2 TATCGCTGAATGAGCC  0
3 AATCGGTGGCACATCT  2
4 GAGTCTCTGGATACAC  1
5 CGACAGTAATCGCTTG  2
6 ACCAGTAGTCAGGTTC  1
7 TAAGCAGGCGTCTTAC  2
> 
> #### with return of alignment probability matrix to R
> #outFile  <- "./countE2.csv"
> #res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
> #    tMat = NULL, numThread = 2, count_only = FALSE,
> #    gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
> #    pen_max = 7)
> #res
> 
> #### user-defined probability model
> comstomizeP <- function(m, x, y)
+ {
+     x * (1 - log(2) + log(1 + m / (m + y) ) )
+ }
> outFile = "comstomizeP.csv"
> bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
+     tMat = NULL, numThread = 2, count_only = TRUE,
+     gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
+     pen_max = 7, userProb = comstomizeP)
Running levenshtein search with 4 sequences per thread in 2 threads
Compiling results
> 
> proc.time()
   user  system elapsed 
   4.42    0.40    4.79 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(bcSeq)
> #devtools::load_all("../")
> #### Set the seed
> set.seed(4523)
> 
> #### Generate barcode
> lFName    <- "./libFile.fasta"
> bases     <- c(rep('A', 4), rep('C',4), rep('G',4), rep('T',4))
> numOfBars <- 7
> Barcodes  <- rep(NA, numOfBars*2)
> for (i in 1:numOfBars){
+     Barcodes[2*i-1] <- paste0(">barcode_ID: ", i)
+     Barcodes[2*i]   <- paste(sample(bases, length(bases)), collapse = '')
+ }
> write(Barcodes, lFName)
> 
> #### Generate reads and phred score
> rFName     <- "./readFile.fastq"
> numOfReads <- 8
> Reads      <- rep(NA, numOfReads*4)
> for (i in 1:numOfReads){
+     Reads[4*i-3] <- paste0("@read_ID_",i)
+     Reads[4*i-2] <- Barcodes[2*sample(1:numOfBars,1,
+                   replace=TRUE, prob=seq(1:numOfBars))]
+     Reads[4*i-1] <- "+"
+     Reads[4*i]   <- paste(rawToChar(as.raw(
+                   33+sample(20:30, length(bases),replace=TRUE))),
+                   collapse='')
+ }
> write(Reads, rFName)
> 
> #### perform alignment 
> ReadFile <- "./readFile.fastq"
> BarFile  <- "./libFile.fasta"
> outFile  <- "./countH.csv"
> 
> #### with default output for bcSeq_hamming
> res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
+     tMat = NULL, numThread = 2, count_only = TRUE )
Running hamming search with 4 sequences per thread in 2 threads
Compiling results
> res <- read.csv(outFile, header=FALSE)
> res
                V1 V2
1 TCCGACGCAAGTGATT  0
2 TATCGCTGAATGAGCC  0
3 AATCGGTGGCACATCT  2
4 GAGTCTCTGGATACAC  1
5 CGACAGTAATCGCTTG  2
6 ACCAGTAGTCAGGTTC  1
7 TAAGCAGGCGTCTTAC  2
> 
> #### with return of alignment probability matrix to R
> #outFile  <- "./countH2.csv"
> #res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
> #    tMat = NULL, numThread = 2, count_only = FALSE )
> #res 
> 
> #### with default output for bcSeq_edit
> outFile  <- "./countE.csv"
> res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
+     tMat = NULL, numThread = 2, count_only = TRUE,
+     gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
+     pen_max = 7)
Running levenshtein search with 4 sequences per thread in 2 threads
Compiling results
> res <- read.csv(outFile, header=FALSE)
> res
                V1 V2
1 TCCGACGCAAGTGATT  0
2 TATCGCTGAATGAGCC  0
3 AATCGGTGGCACATCT  2
4 GAGTCTCTGGATACAC  1
5 CGACAGTAATCGCTTG  2
6 ACCAGTAGTCAGGTTC  1
7 TAAGCAGGCGTCTTAC  2
> 
> #### with return of alignment probability matrix to R
> #outFile  <- "./countE2.csv"
> #res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
> #    tMat = NULL, numThread = 2, count_only = FALSE,
> #    gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
> #    pen_max = 7)
> #res
> 
> #### user-defined probability model
> comstomizeP <- function(m, x, y)
+ {
+     x * (1 - log(2) + log(1 + m / (m + y) ) )
+ }
> outFile = "comstomizeP.csv"
> bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
+     tMat = NULL, numThread = 2, count_only = TRUE,
+     gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
+     pen_max = 7, userProb = comstomizeP)
Running levenshtein search with 4 sequences per thread in 2 threads
Compiling results
> 
> proc.time()
   user  system elapsed 
   4.45    0.15    4.57