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对bwa-mem过程进行加速优化
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Heng Li 8f0d439913 prepare to replace the SAM printing code 
This move is dangerous as SAM printing is very complex, but it will benefit in
the long run. The planned change will reduce the redundancy, improves clarity
and most importantly makes it much easier to output multiple primary hits in an
optional tag.
 		2013-03-11 21:25:17 -04:00
.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 r342: bugfix in bwasw - AS is off by one 2013-03-08 12:06:45 -05:00
NEWS Release bwa-0.7.2-r351 2013-03-09 18:15:41 -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 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 r334: added pemerge to bwa 2013-03-06 21:55:02 -05:00
bntseq.h r283: prepare for fixing cross-ref aln 2013-02-25 22:49:15 -05:00
bwa.1 Release bwa-0.7.2-r351 2013-03-09 18:15:41 -05:00
bwa.c Match to 'N' costs -1, instead of 0. 2013-03-09 18:03:57 -05:00
bwa.h move mem_fill_scmat() to bwa.{h,c} 2013-03-05 09:38:12 -05:00
bwamem.c prepare to replace the SAM printing code 2013-03-11 21:25:17 -04:00
bwamem.h prepare to replace the SAM printing code 2013-03-11 21:25:17 -04:00
bwamem_pair.c Improving 'properly paired' flag. 2013-03-09 18:05:50 -05:00
bwape.c r329: ditch stdaln.{c,h}; no changes to bwa-mem 2013-03-05 12:00:24 -05:00
bwase.c r336: fine tuning pemerge 2013-03-06 23:38:07 -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 cleanup bwt_occ() 2013-02-26 12:09:28 -05:00
bwt.h Updated NEWS; added stddef.h for size_t 2013-03-08 14:14:42 -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 r329: ditch stdaln.{c,h}; no changes to bwa-mem 2013-03-05 12:00:24 -05:00
bwtaln.h r329: ditch stdaln.{c,h}; no changes to bwa-mem 2013-03-05 12:00:24 -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 r335: fixed a compiling error 2013-03-06 21:57:13 -05:00
bwtsw2.h r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -04:00
bwtsw2_aux.c r342: bugfix in bwasw - AS is off by one 2013-03-08 12:06:45 -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 cleanup index loading code 2013-02-23 16:10:48 -05:00
bwtsw2_pair.c prepare to ditch stdaln.{h,c} 2013-03-04 10:32:33 -05:00
example.c r314: cleanup bwamem API 2013-03-01 11:14:51 -05:00
fastmap.c r340: feature freeze; updated the manpage 2013-03-07 11:51:23 -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
kopen.c cleanup bwt_occ() 2013-02-26 12:09:28 -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 prepare to replace the SAM printing code 2013-03-11 21:25:17 -04:00
ksw.c bwa-sw: ditch stdaln 2013-03-05 10:12:38 -05:00
ksw.h r323: added Z-dropoff, a variant of blast's X-drop 2013-03-05 00:34:33 -05:00
kvec.h generate multiple alignments from one chain 2013-02-21 14:58:51 -05:00
main.c Release bwa-0.7.2-r351 2013-03-09 18:15:41 -05:00
pemerge.c r339: pemerge - expose some settings to CLI 2013-03-07 11:22:19 -05:00
qualfa2fq.pl Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
utils.c moved some common code to bwa.{c,h} 2013-02-23 15:30:46 -05:00
utils.h moved some common code to bwa.{c,h} 2013-02-23 15:30:46 -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