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对bwa-mem过程进行加速优化
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Heng Li ee80fb8bd0 Test each seed to see if extension is needed 
The old version wastefully extends many seeds contained in an aligned region
found before. While this wastes little time for short reads, it becomes a
serious defect for long query sequences.

This is an attempt to fix this problem, but more tuning are needed.
 		2013-02-26 22:55:44 -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 change CC back to gcc 2013-02-24 23:45:40 -05:00
NEWS r126: release bwa-0.6.2 2012-06-19 13:29:44 -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 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 r283: prepare for fixing cross-ref aln 2013-02-25 22:49:15 -05:00
bntseq.h r283: prepare for fixing cross-ref aln 2013-02-25 22:49:15 -05:00
bwa.1 r126: release bwa-0.6.2 2012-06-19 13:29:44 -04:00
bwa.c r295: generate NM 2013-02-26 13:36:01 -05:00
bwa.h r295: generate NM 2013-02-26 13:36:01 -05:00
bwamem.c Test each seed to see if extension is needed 2013-02-26 22:55:44 -05:00
bwamem.h r292: fixed a very stupid bug on CLI 2013-02-26 12:49:48 -05:00
bwamem_pair.c r284: amend cross-reference hit 2013-02-26 00:03:49 -05:00
bwape.c support read group in bwa-mem 2013-02-23 16:41:44 -05:00
bwase.c fixed a couple bugs identified by gcc 2013-02-23 17:15:07 -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 move bwt_invPsi() from bwt.h to bwt.c 2013-02-26 11:57:36 -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 cleanup index loading code 2013-02-23 16:10:48 -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 moved some common code to bwa.{c,h} 2013-02-23 15:30:46 -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 bugfix: bug in the new ksw.c 2013-02-12 17:48:46 -05:00
fastmap.c r295: generate NM 2013-02-26 13:36:01 -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 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 r297: reduce wasteful SW extension 2013-02-26 16:26:46 -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
stdaln.c removed a few unused variables 2013-02-23 13:26:50 -05:00
stdaln.h 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