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对bwa-mem过程进行加速优化
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Heng Li 9a6abe51b6 r391: better method to resolve xref alignment 
The old method does not work when the alignment bridges three chr. This may
actually happen often. The new method does not work all the time, either, but
should be better than the old one. It is also simpler, arguably.
 		2013-05-22 18:57:51 -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 r391: better method to resolve xref alignment 2013-05-22 18:57:51 -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 r391: better method to resolve xref alignment 2013-05-22 18:57:51 -04:00
bwa.h move mem_fill_scmat() to bwa.{h,c} 2013-03-05 09:38:12 -05:00
bwamem.c r391: better method to resolve xref alignment 2013-05-22 18:57:51 -04:00
bwamem.h r388: cleanup mem_process_seqs() interface 2013-04-26 12:31:18 -04:00
bwamem_pair.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bwape.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bwase.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
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 Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bwtaln.h r329: ditch stdaln.{c,h}; no changes to bwa-mem 2013-03-05 12:00:24 -05:00
bwtgap.c Reduce dependency on utils.h - new malloc wrapping scheme. 2013-05-02 15:12:01 +01:00
bwtgap.h API: aln seems working 2012-04-07 00:23:01 -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 Ensure exit status of 1 if given invalid options or index files are not found. 2013-04-29 13:58:28 +01:00
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 r391: better method to resolve xref alignment 2013-05-22 18:57:51 -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