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对bwa-mem过程进行加速优化
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Heng Li 6476343a83 r331: rewrote CIGAR generation for bwa-short 
When backtracking, bwa-short does not keep the detailed alignment or the exact
start and end positions. To find the boundary and the CIGAR, the old code does
a global alignment with a small end-gap penalty. It then deals with a lot of
special cases to derive the right position and CIGAR, which are actually not
always right. It is a mess.

As the new ksw.{c,h} does not support a different end-gap penalty, the old
strategy does not work. But we get something better. The new code finds the
boundaries with ksw_extend(). It is cleaner and gives more accurate CIGAR in
most cases.
 		2013-03-05 19:56:37 -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 Fixing problem with linking to libm on some Ubuntu systems (I see this on machine running 11.04, kernel 3.0.0-14-virtual). Changing order of -lm on the command line seems to do the trick and should be tolerated in other environments. 2013-03-05 20:48:16 +00:00
NEWS r313: release bwa-0.7.0 2013-02-28 15:56:05 -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 r316: don't allocate zero-length memory 2013-03-04 10:22:18 -05:00
bntseq.h r283: prepare for fixing cross-ref aln 2013-02-25 22:49:15 -05:00
bwa.1 r306: introduce clipping penalty 2013-02-27 21:13:39 -05:00
bwa.c move mem_fill_scmat() to bwa.{h,c} 2013-03-05 09:38:12 -05:00
bwa.h move mem_fill_scmat() to bwa.{h,c} 2013-03-05 09:38:12 -05:00
bwamem.c move mem_fill_scmat() to bwa.{h,c} 2013-03-05 09:38:12 -05:00
bwamem.h r324: a little code cleanup 2013-03-05 00:57:16 -05:00
bwamem_pair.c r284: amend cross-reference hit 2013-02-26 00:03:49 -05:00
bwape.c r329: ditch stdaln.{c,h}; no changes to bwa-mem 2013-03-05 12:00:24 -05:00
bwase.c r331: rewrote CIGAR generation for bwa-short 2013-03-05 19:56:37 -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 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 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 bwa-sw: ditch stdaln 2013-03-05 10:12:38 -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 move mem_fill_scmat() to bwa.{h,c} 2013-03-05 09:38:12 -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 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 r331: rewrote CIGAR generation for bwa-short 2013-03-05 19:56:37 -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
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