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基于bwa，做一些优化，注释
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Heng Li 599e840779 r397: multi changes/bugfixes to bwa-backtrack 
1. Check .sai versioning
2. Keep track of #ins and #del during backtrack
3. Use info above to get accurate aligned regions; don't call SW extension any more
4. Identify alignment crossing the for-rev boundary
5. Fixed a bug in printing the XA tag: ungapped alignments missing
 		2013-05-24 16:28:18 -04:00
.gitignore Added Makefile.bak and bwamem-lite to .gitignore 2013-03-13 09:18:18 +00:00
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Makefile conform to the latest (unpublished) SAM spec 2013-05-22 19:45:16 -04:00
NEWS r386: typo in NEWS 2013-04-23 12:30:22 -04:00
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 Removed more dependencies on utils.h 2013-05-03 11:38:48 +01:00
bamlite.h Removed more dependencies on utils.h 2013-05-03 11:38:48 +01:00
bntseq.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bntseq.h r283: prepare for fixing cross-ref aln 2013-02-25 22:49:15 -05:00
bwa.1 Released bwa-0.7.4-r385 2013-04-23 11:40:56 -04:00
bwa.c conform to the latest (unpublished) SAM spec 2013-05-22 19:45:16 -04:00
bwa.h move mem_fill_scmat() to bwa.{h,c} 2013-03-05 09:38:12 -05:00
bwamem.c r396: er... the new tag is named SA not SP 2013-05-23 12:48:18 -04:00
bwamem.h conform to the latest (unpublished) SAM spec 2013-05-22 19:45:16 -04:00
bwamem_pair.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bwape.c r397: multi changes/bugfixes to bwa-backtrack 2013-05-24 16:28:18 -04:00
bwase.c r397: multi changes/bugfixes to bwa-backtrack 2013-05-24 16:28:18 -04:00
bwase.h removed color-space support 2013-02-12 10:21:17 -05:00
bwaseqio.c Removed more dependencies on utils.h 2013-05-03 11:38:48 +01:00
bwt.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bwt.h Updated NEWS; added stddef.h for size_t 2013-03-08 14:14:42 -05:00
bwt_gen.c Removed more dependencies on utils.h 2013-05-03 11:38:48 +01:00
bwt_lite.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bwt_lite.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bwtaln.c r397: multi changes/bugfixes to bwa-backtrack 2013-05-24 16:28:18 -04:00
bwtaln.h r397: multi changes/bugfixes to bwa-backtrack 2013-05-24 16:28:18 -04:00
bwtgap.c r397: multi changes/bugfixes to bwa-backtrack 2013-05-24 16:28:18 -04:00
bwtgap.h r397: multi changes/bugfixes to bwa-backtrack 2013-05-24 16:28:18 -04:00
bwtindex.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bwtsw2.h r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -04:00
bwtsw2_aux.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bwtsw2_chain.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bwtsw2_core.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bwtsw2_main.c Ensure exit status of 1 if given invalid options or index files are not found. 2013-04-29 13:58:28 +01:00
bwtsw2_pair.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
example.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
fastmap.c conform to the latest (unpublished) SAM spec 2013-05-22 19:45:16 -04:00
is.c Removed more dependencies on utils.h 2013-05-03 11:38:48 +01:00
kbtree.h Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
khash.h Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
kopen.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
kseq.h Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
ksort.h Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
kstring.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
kstring.h Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
ksw.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
ksw.h Removed more dependencies on utils.h 2013-05-03 11:38:48 +01:00
kvec.h Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
main.c r397: multi changes/bugfixes to bwa-backtrack 2013-05-24 16:28:18 -04:00
malloc_wrap.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
malloc_wrap.h Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
pemerge.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
qualfa2fq.pl Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
utils.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
utils.h Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
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