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基于bwa，做一些优化，注释
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Rob Davies b081ac9b8b Use wrapper functions to catch system errors 
Use the wrapper functions in utils.c plus a few extra bits of error
checking code to catch system errors and exit non-zero when they occur.
 		2012-12-16 10:34:57 +00:00
.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 Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
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 Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bamlite.h Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bntseq.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
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 Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwa.h updated APIs abit 2012-04-08 00:55:52 -04:00
bwape.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwase.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwase.h PE seems working; more testing needed 2011-10-20 17:45:41 -04:00
bwaseqio.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwt.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwt.h fixed a deadlock; SMEM iterator 2011-11-24 19:15:14 -05:00
bwt_gen.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwt_lite.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwt_lite.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bwtaln.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwtaln.h preliminary doc 2012-04-07 22:50:07 -04:00
bwtgap.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwtgap.h API: aln seems working 2012-04-07 00:23:01 -04:00
bwtindex.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwtio.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwtmisc.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwtsw2.h r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -04:00
bwtsw2_aux.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwtsw2_chain.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwtsw2_core.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
bwtsw2_main.c r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -04:00
bwtsw2_pair.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
cs2nt.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
fastmap.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
is.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
khash.h Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
kseq.h Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
ksort.h Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
kstring.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
kstring.h Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
ksw.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
ksw.h mate rescue seems working (not MT) 2011-11-06 16:20:40 -05:00
kvec.h Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
main.c r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -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 Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
solid2fastq.pl Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
stdaln.c Use wrapper functions to catch system errors 2012-12-16 10:34:57 +00:00
stdaln.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
utils.c Added more wrappers for functions that make system calls 2012-12-16 10:05:32 +00:00
utils.h Added more wrappers for functions that make system calls 2012-12-16 10:05:32 +00:00
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