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对bwa-mem过程进行加速优化
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Heng Li 2087dc162f r377: increased unpaired penalty from 9 to 17 
This leads to more aggressive pairing - more properly paired reads. I have
found a few cases where, for example, read1 is umambiguously mapped to chr20
while its 100bp mate has a perfect match to another chr but has 3 mismatches
and 1 deletion when it is paired with read1 on chr20. With longer reads, it
seems that the chr20 hit is correct, although it is not obvious how this
happened in evolution.
 		2013-04-17 16:50:20 -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-0.7.3a-r367 2013-03-15 21:26:37 -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 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 r377: increased unpaired penalty from 9 to 17 2013-04-17 16:50:20 -04:00
bwa.c r368: bugfix - wrong CIGAR when bridging 3 contigs 2013-03-18 20:49:32 -04:00
bwa.h move mem_fill_scmat() to bwa.{h,c} 2013-03-05 09:38:12 -05:00
bwamem.c r377: increased unpaired penalty from 9 to 17 2013-04-17 16:50:20 -04:00
bwamem.h r373: optionally distable mate rescue 2013-04-09 16:13:55 -04:00
bwamem_pair.c r373: optionally distable mate rescue 2013-04-09 16:13:55 -04:00
bwape.c r329: ditch stdaln.{c,h}; no changes to bwa-mem 2013-03-05 12:00:24 -05:00
bwase.c r375: fixed compiling errors by the last change 2013-04-10 11:04:32 -04:00
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 fixed an issue caused by a Mac/Darwin bug 2013-04-09 15:17:04 -04:00
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 r375: fixed compiling errors by the last change 2013-04-10 11:04:32 -04:00
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 r359: identical output to 0.7.2 (without -a) 2013-03-11 23:16:18 -04:00
fastmap.c r373: optionally distable mate rescue 2013-04-09 16:13:55 -04:00
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 r374: fix - clipping penalty not always working 2013-04-10 01:09:37 -04:00
ksw.h r374: fix - clipping penalty not always working 2013-04-10 01:09:37 -04:00
kvec.h generate multiple alignments from one chain 2013-02-21 14:58:51 -05:00
main.c r377: increased unpaired penalty from 9 to 17 2013-04-17 16:50:20 -04:00
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