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基于bwa，做一些优化，注释
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Heng Li 6230f86799 merged bwtmisc.c to bwtindex.c 
bwtmisc.c implements routines related to indexing
 		2013-02-22 17:23:34 -05:00
.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 merged bwtmisc.c to bwtindex.c 2013-02-22 17:23:34 -05:00
NEWS r126: release bwa-0.6.2 2012-06-19 13:29:44 -04:00
QSufSort.c move bwt_gen/* to the root directory 2011-10-20 11:56:24 -04:00
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 Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bamlite.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bntseq.c forbid x-bounary bns_get_seq(); code backup 2013-02-16 09:48:44 -05:00
bntseq.h code backup 2013-02-11 10:59:38 -05:00
bwa.1 r126: release bwa-0.6.2 2012-06-19 13:29:44 -04:00
bwamem.c pring paired-end SAM 2013-02-22 16:38:48 -05:00
bwamem.h pring paired-end SAM 2013-02-22 16:38:48 -05:00
bwamem_pair.c pring paired-end SAM 2013-02-22 16:38:48 -05:00
bwape.c code backup 2013-02-12 12:09:36 -05:00
bwase.c minor code clean up 2013-02-22 17:09:40 -05:00
bwase.h removed color-space support 2013-02-12 10:21:17 -05:00
bwaseqio.c updated to the latest kseq.h 2013-02-06 14:38:40 -05:00
bwt.c minor code clean up 2013-02-22 17:09:40 -05:00
bwt.h move smem iterators to bwamem.{c,h} 2013-01-31 13:59:48 -05:00
bwt_gen.c print msg to stderr; output more in fastmap 2011-10-25 15:06:13 -04:00
bwt_lite.c Do not inline functions used externally 2012-06-25 12:48:43 -07:00
bwt_lite.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bwtaln.c removed color-space support 2013-02-12 10:21:17 -05:00
bwtaln.h removed color-space support 2013-02-12 10:21:17 -05:00
bwtgap.c API: aln seems working 2012-04-07 00:23:01 -04:00
bwtgap.h API: aln seems working 2012-04-07 00:23:01 -04:00
bwtindex.c merged bwtmisc.c to bwtindex.c 2013-02-22 17:23:34 -05:00
bwtsw2.h r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -04:00
bwtsw2_aux.c merge bseq.{h,c} to utils.{h,c} 2013-02-12 10:36:15 -05:00
bwtsw2_chain.c r128: more conservative chaining filter 2012-06-28 14:51:02 -04:00
bwtsw2_core.c mate rescue seems working (not MT) 2011-11-06 16:20:40 -05:00
bwtsw2_main.c r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -04:00
bwtsw2_pair.c bugfix: bug in the new ksw.c 2013-02-12 17:48:46 -05:00
fastmap.c minor code clean up 2013-02-22 17:09:40 -05:00
is.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kbtree.h code cleanup; added a missing file 2013-02-01 14:38:44 -05:00
khash.h Multiple changes: 2013-02-12 09:50:28 -05:00
kseq.h updated to the latest kseq.h 2013-02-06 14:38:40 -05:00
ksort.h code backup 2013-02-12 09:22:47 -05:00
kstring.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kstring.h separated and improved SAM printing code 2013-02-11 15:29:03 -05:00
ksw.c clean bill from valgrind 2013-02-20 20:26:57 -05:00
ksw.h updated to the latest ksw; NOT TESTED YET!!! 2013-02-12 16:35:05 -05:00
kvec.h generate multiple alignments from one chain 2013-02-21 14:58:51 -05:00
main.c removed another part related to color-space 2013-02-22 17:15:57 -05:00
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
solid2fastq.pl Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
stdaln.c use standard SW when no SSE2 2011-11-19 19:38:21 -05:00
stdaln.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
utils.c minor code clean up 2013-02-22 17:09:40 -05:00
utils.h code backup 2013-02-12 12:09:36 -05:00
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