View source for Benchmarking: BWA 0.7.12 - Burrows-Wheeler Aligner

* Download 0.7.12 from: wget 'http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.12.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbio-bwa%2F&ts=1424211953&use_mirror=switch'

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[david@head-Boston bwa]$ tar jxvf bwa-0.7.12.tar.bz2 
bwa-0.7.12/
bwa-0.7.12/bamlite.c
bwa-0.7.12/bamlite.h
bwa-0.7.12/bntseq.c
bwa-0.7.12/bntseq.h
bwa-0.7.12/bwa.1
bwa-0.7.12/bwa.c
bwa-0.7.12/bwa.h
bwa-0.7.12/bwakit/
bwa-0.7.12/bwamem.c
bwa-0.7.12/bwamem.h
bwa-0.7.12/bwamem_extra.c
bwa-0.7.12/bwamem_pair.c
bwa-0.7.12/bwape.c
bwa-0.7.12/bwase.c
bwa-0.7.12/bwase.h
bwa-0.7.12/bwaseqio.c
bwa-0.7.12/bwashm.c
bwa-0.7.12/bwt.c
bwa-0.7.12/bwt.h
bwa-0.7.12/bwt_gen.c
bwa-0.7.12/bwt_lite.c
bwa-0.7.12/bwt_lite.h
bwa-0.7.12/bwtaln.c
bwa-0.7.12/bwtaln.h
bwa-0.7.12/bwtgap.c
bwa-0.7.12/bwtgap.h
bwa-0.7.12/bwtindex.c
bwa-0.7.12/bwtsw2.h
bwa-0.7.12/bwtsw2_aux.c
bwa-0.7.12/bwtsw2_chain.c
bwa-0.7.12/bwtsw2_core.c
bwa-0.7.12/bwtsw2_main.c
bwa-0.7.12/bwtsw2_pair.c
bwa-0.7.12/ChangeLog
bwa-0.7.12/COPYING
bwa-0.7.12/example.c
bwa-0.7.12/fastmap.c
bwa-0.7.12/is.c
bwa-0.7.12/kbtree.h
bwa-0.7.12/khash.h
bwa-0.7.12/kopen.c
bwa-0.7.12/kseq.h
bwa-0.7.12/ksort.h
bwa-0.7.12/kstring.c
bwa-0.7.12/kstring.h
bwa-0.7.12/ksw.c
bwa-0.7.12/ksw.h
bwa-0.7.12/kthread.c
bwa-0.7.12/kvec.h
bwa-0.7.12/main.c
bwa-0.7.12/Makefile
bwa-0.7.12/malloc_wrap.c
bwa-0.7.12/malloc_wrap.h
bwa-0.7.12/NEWS.md
bwa-0.7.12/pemerge.c
bwa-0.7.12/QSufSort.c
bwa-0.7.12/QSufSort.h
bwa-0.7.12/qualfa2fq.pl
bwa-0.7.12/README-alt.md
bwa-0.7.12/README.md
bwa-0.7.12/utils.c
bwa-0.7.12/utils.h
bwa-0.7.12/xa2multi.pl
bwa-0.7.12/bwakit/bwa-postalt.js
bwa-0.7.12/bwakit/README.md
bwa-0.7.12/bwakit/run-bwamem
bwa-0.7.12/bwakit/run-gen-ref
bwa-0.7.12/bwakit/run-HLA
bwa-0.7.12/bwakit/typeHLA-selctg.js
bwa-0.7.12/bwakit/typeHLA.js
bwa-0.7.12/bwakit/typeHLA.sh
[david@head-Boston bwa]$ ls
bwa-0.7.12  bwa-0.7.12.tar.bz2
[david@head-Boston bwa]$ cd bwa-0.7.12
[david@head-Boston bwa-0.7.12]$ ls
bamlite.c  bwa.h           bwape.c     bwtaln.h   bwtindex.c      bwtsw2.h       fastmap.c  ksort.h    kvec.h         pemerge.c      utils.c
bamlite.h  bwakit          bwase.c     bwt.c      bwt_lite.c      bwtsw2_main.c  is.c       kstring.c  main.c         QSufSort.c     utils.h
bntseq.c   bwamem.c        bwase.h     bwtgap.c   bwt_lite.h      bwtsw2_pair.c  kbtree.h   kstring.h  Makefile       QSufSort.h     xa2multi.pl
bntseq.h   bwamem_extra.c  bwaseqio.c  bwtgap.h   bwtsw2_aux.c    ChangeLog      khash.h    ksw.c      malloc_wrap.c  qualfa2fq.pl
bwa.1      bwamem.h        bwashm.c    bwt_gen.c  bwtsw2_chain.c  COPYING        kopen.c    ksw.h      malloc_wrap.h  README-alt.md
bwa.c      bwamem_pair.c   bwtaln.c    bwt.h      bwtsw2_core.c   example.c      kseq.h     kthread.c  NEWS.md        README.md
[david@head-Boston bwa-0.7.12]$ make 
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  utils.c -o utils.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kthread.c -o kthread.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kstring.c -o kstring.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt.c -o bwt.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bntseq.c -o bntseq.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwa.c -o bwa.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem.c -o bwamem.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem_pair.c -o bwamem_pair.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem_extra.c -o bwamem_extra.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  malloc_wrap.c -o malloc_wrap.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  QSufSort.c -o QSufSort.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt_gen.c -o bwt_gen.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwashm.c -o bwashm.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwase.c -o bwase.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwaseqio.c -o bwaseqio.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtgap.c -o bwtgap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtaln.c -o bwtaln.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bamlite.c -o bamlite.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  is.c -o is.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtindex.c -o bwtindex.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwape.c -o bwape.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kopen.c -o kopen.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  pemerge.c -o pemerge.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_core.c -o bwtsw2_core.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt_lite.c -o bwt_lite.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_chain.c -o bwtsw2_chain.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  fastmap.c -o fastmap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_pair.c -o bwtsw2_pair.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  main.c -o main.o
gcc -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
[david@head-Boston bwa-0.7.12]$ ls
bamlite.c  bwa.h           bwa.o       bwashm.o   bwt_gen.o     bwtsw2_aux.o    bwtsw2_pair.o  khash.h    ksw.h      malloc_wrap.c  qualfa2fq.pl
bamlite.h  bwakit          bwape.c     bwtaln.c   bwt.h         bwtsw2_chain.c  ChangeLog      kopen.c    ksw.o      malloc_wrap.h  README-alt.md
bamlite.o  bwamem.c        bwape.o     bwtaln.h   bwtindex.c    bwtsw2_chain.o  COPYING        kopen.o    kthread.c  malloc_wrap.o  README.md
bntseq.c   bwamem_extra.c  bwase.c     bwtaln.o   bwtindex.o    bwtsw2_core.c   example.c      kseq.h     kthread.o  NEWS.md        utils.c
bntseq.h   bwamem_extra.o  bwase.h     bwt.c      bwt_lite.c    bwtsw2_core.o   fastmap.c      ksort.h    kvec.h     pemerge.c      utils.h
bntseq.o   bwamem.h        bwase.o     bwtgap.c   bwt_lite.h    bwtsw2.h        fastmap.o      kstring.c  libbwa.a   pemerge.o      utils.o
bwa        bwamem.o        bwaseqio.c  bwtgap.h   bwt_lite.o    bwtsw2_main.c   is.c           kstring.h  main.c     QSufSort.c     xa2multi.pl
bwa.1      bwamem_pair.c   bwaseqio.o  bwtgap.o   bwt.o         bwtsw2_main.o   is.o           kstring.o  main.o     QSufSort.h
bwa.c      bwamem_pair.o   bwashm.c    bwt_gen.c  bwtsw2_aux.c  bwtsw2_pair.c   kbtree.h       ksw.c      Makefile   QSufSort.o
[david@head-Boston bwa-0.7.12]$ ./bwa

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.12-r1039
Contact: Heng Li <lh3@sanger.ac.uk>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         shm           manage indices in shared memory
         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
      There are three alignment algorithms in BWA: `mem', `bwasw', and
      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
      first. Please `man ./bwa.1' for the manual.


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