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对bwa-mem过程进行加速优化
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Rob Davies 55f1b36534 New wrapper for gzclose; added err_fflush calls and made it call fsync too. 
Added a new utils.c wrapper err_gzclose and changed gzclose calls to use it.

Put in some more err_fflush calls before files being written are closed.

Made err_fflush call fsync.  This is useful for remote filesystems where
errors may not be reported on fflush or fclose as problems at the server
end may only be detected after they have returned.  If bwa is being used
only to write to local filesystems, calling fsync is not really necessary.
To disable it, comment out #define FSYNC_ON_FLUSH in utils.c.
 		2013-01-03 16:57:37 +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 New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +00:00
bntseq.c New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +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 New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +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 unnecessary large .sai output 2012-04-17 19:31:37 -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 New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +00:00
bwtio.c New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +00:00
bwtmisc.c New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +00:00
bwtsw2.h r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -04:00
bwtsw2_aux.c New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +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 New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +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 New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +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 New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +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 New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +00:00
utils.h New wrapper for gzclose; added err_fflush calls and made it call fsync too. 2013-01-03 16:57:37 +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