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基于bwa，做一些优化，注释
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C 90.9%
JavaScript 3.5%
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Rob Davies 6beab5f765 Merge branch 'master' into master_fixes 
Merge changes to commit c5434ac (0.7.0 release)

Conflicts:
	Makefile
	bwamem.c
 		2013-03-01 10:22:49 +00:00
.gitignore to exclude "test64" 2013-02-12 10:39:16 -05:00
COPYING Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
ChangeLog Update to the latest modfication 0.5.9rc1-2. Update ChangeLog 2011-01-13 20:54:10 -05:00
Makefile Merge branch 'master' into master_fixes 2013-03-01 10:22:49 +00:00
NEWS r313: release bwa-0.7.0 2013-02-28 15:56:05 -05:00
QSufSort.c removed a few unused variables 2013-02-23 13:26:50 -05:00
QSufSort.h move bwt_gen/* to the root directory 2011-10-20 11:56:24 -04:00
README added SEAL 2011-11-12 20:48:35 -05:00
bamlite.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bamlite.h New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +00:00
bntseq.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
bntseq.h r283: prepare for fixing cross-ref aln 2013-02-25 22:49:15 -05:00
bwa.1 r306: introduce clipping penalty 2013-02-27 21:13:39 -05:00
bwa.c Merge branch 'master' into master_fixes 2013-03-01 10:22:49 +00:00
bwa.h r295: generate NM 2013-02-26 13:36:01 -05:00
bwamem.c Merge branch 'master' into master_fixes 2013-03-01 10:22:49 +00:00
bwamem.h r309: bugfix - soft clipping missing in example.c 2013-02-27 22:45:18 -05:00
bwamem_pair.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
bwape.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
bwase.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
bwase.h removed color-space support 2013-02-12 10:21:17 -05:00
bwaseqio.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
bwt.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
bwt.h move bwt_invPsi() from bwt.h to bwt.c 2013-02-26 11:57:36 -05:00
bwt_gen.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
bwt_lite.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwt_lite.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bwtaln.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
bwtaln.h removed color-space support 2013-02-12 10:21:17 -05:00
bwtgap.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwtgap.h API: aln seems working 2012-04-07 00:23:01 -04:00
bwtindex.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
bwtsw2.h r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -04:00
bwtsw2_aux.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
bwtsw2_chain.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwtsw2_core.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwtsw2_main.c cleanup index loading code 2013-02-23 16:10:48 -05:00
bwtsw2_pair.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
example.c Merge branch 'master' into master_fixes 2013-03-01 10:22:49 +00:00
fastmap.c Merge branch 'master' into master_fixes 2013-03-01 10:22:49 +00:00
is.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
kbtree.h Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
khash.h Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
kopen.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
kseq.h Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
ksort.h Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
kstring.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
kstring.h Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
ksw.c Merge branch 'master' into master_fixes 2013-03-01 10:22:49 +00:00
ksw.h more documentation in ksw.h 2013-02-27 21:40:46 -05:00
kvec.h Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
main.c Merge branch 'master' into master_fixes 2013-03-01 10:22:49 +00:00
main.h removed another part related to color-space 2013-02-22 17:15:57 -05:00
qualfa2fq.pl Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
stdaln.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
stdaln.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
utils.c Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
utils.h Merge branch 'master' into master_fixes 2013-03-01 09:37:46 +00:00
xa2multi.pl Bugfix: reverse (complement) sequence and phred string if alternative alignment has different orientation than primary alignment 2011-09-07 14:31:28 +02:00

README 

Released packages can be downloaded from SourceForge.net:

  http://sourceforge.net/projects/bio-bwa/files/

Introduction and FAQ are available at:

  http://bio-bwa.sourceforge.net

Manual page at:

  http://bio-bwa.sourceforge.net/bwa.shtml

Mailing list:

  bio-bwa-help@lists.sourceforge.net

To sign up:

  http://sourceforge.net/mail/?group_id=276243

Publications (Open Access):

  http://www.ncbi.nlm.nih.gov/pubmed/20080505
  http://www.ncbi.nlm.nih.gov/pubmed/19451168

Incomplete list of citations (via HubMed.org):

  http://www.hubmed.org/references.cgi?uids=20080505
  http://www.hubmed.org/references.cgi?uids=19451168

Related projects:

  http://pbwa.sourceforge.net/
  http://www.many-core.group.cam.ac.uk/projects/lam.shtml
  http://biodoop-seal.sourceforge.net/
  http://gitorious.org/bwa-cuda