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对bwa-mem过程进行加速优化
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Shaun Jackman 84d34e1d0b Do not inline functions used externally 
Compiling using CLANG gives the following errors:
Undefined symbols for architecture x86_64:
  "_bwt_occ", referenced from:
      _bwt_cal_sa in bwt.o
      _bwt_sa in bwt.o
  "_bwt_2occ", referenced from:
      _bwt_match_exact in bwt.o
      _bwt_match_exact_alt in bwt.o
      _bwt_cal_width in bwtaln.o
  "_bwt_2occ4", referenced from:
      _bwt_match_gap in bwtgap.o
      _bsw2_core in bwtsw2_core.o
  "_bwtl_2occ4", referenced from:
      _bsw2_core in bwtsw2_core.o
 		2012-06-25 12:48:43 -07:00
.gitignore Added barcode support 2011-01-15 15:35:39 -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 compute CIGAR; rev seq not working 2012-04-07 22:00:03 -04:00
NEWS r126: release bwa-0.6.2 2012-06-19 13:29:44 -04:00
QSufSort.c move bwt_gen/* to the root directory 2011-10-20 11:56:24 -04:00
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 fixed a segfault when there are too few good bases. 2011-11-17 22:13:38 -05:00
bntseq.h fixed a minor issue about +/-1 2011-10-25 13:00:41 -04:00
bwa.1 r126: release bwa-0.6.2 2012-06-19 13:29:44 -04:00
bwa.c updated APIs abit 2012-04-08 00:55:52 -04:00
bwa.h updated APIs abit 2012-04-08 00:55:52 -04:00
bwape.c Tim's suggestion suffix file name with .64 2012-03-29 12:22:51 -04:00
bwase.c compute CIGAR; rev seq not working 2012-04-07 22:00:03 -04:00
bwase.h PE seems working; more testing needed 2011-10-20 17:45:41 -04:00
bwaseqio.c fixed a minor issue in trimming 2011-11-24 10:39:41 -05:00
bwt.c Do not inline functions used externally 2012-06-25 12:48:43 -07:00
bwt.h fixed a deadlock; SMEM iterator 2011-11-24 19:15:14 -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 API: aln seems working 2012-04-07 00:23:01 -04:00
bwtaln.h unnecessary large .sai output 2012-04-17 19:31:37 -04:00
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 do not use .64 suffix by default 2012-03-29 12:31:01 -04:00
bwtio.c make changes to bwt.c 2011-10-19 17:42:42 -04:00
bwtmisc.c removed reverse pac; bwa is not working right now 2011-10-20 12:09:35 -04:00
bwtsw2.h r115: added -I and -S to bwasw 2012-04-17 20:43:43 -04:00
bwtsw2_aux.c r115: added -I and -S to bwasw 2012-04-17 20:43:43 -04:00
bwtsw2_chain.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bwtsw2_core.c mate rescue seems working (not MT) 2011-11-06 16:20:40 -05:00
bwtsw2_main.c r115: added -I and -S to bwasw 2012-04-17 20:43:43 -04:00
bwtsw2_pair.c r115: added -I and -S to bwasw 2012-04-17 20:43:43 -04:00
cs2nt.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
fastmap.c fastmap: optionally output the original query seq 2011-11-24 19:44:21 -05:00
is.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
khash.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kseq.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
ksort.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kstring.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kstring.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
ksw.c use standard SW when no SSE2 2011-11-19 19:38:21 -05:00
ksw.h mate rescue seems working (not MT) 2011-11-06 16:20:40 -05:00
kvec.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
main.c r126: release bwa-0.6.2 2012-06-19 13:29:44 -04:00
main.h added bidirectional bwt; seems buggy 2011-10-25 00:22:28 -04:00
qualfa2fq.pl Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
simple_dp.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
solid2fastq.pl Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
stdaln.c use standard SW when no SSE2 2011-11-19 19:38:21 -05:00
stdaln.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
utils.c multithreading works again 2011-11-12 16:50:58 -05:00
utils.h multithreading works again 2011-11-12 16:50:58 -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