zzh
/
bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
对bwa-mem过程进行加速优化
142 Commits
1 Branch
0 Tags
1.8 MiB
C 86.8%
JavaScript 5.3%
Roff 4%
C++ 1.4%
Perl 1.2%
Other 1.3%
 
 
 
 
 
 
Go to file
Rob Davies 4f4e998d7f Added wrappers for fputc and fputs; more efficient sequence printing 
Added wrappers err_fputc and err_fputs to catch failures in fput and fputs.
Macros err_putchar and err_puts call the new wrappers and can be used in
place of putchar and puts.

To avoid having to make millions of function calls when printing out
sequences, the code to print them in bwa_print_sam1 using putchar has
been replaced by a new version in bwa_print_seq that puts the sequence
into a buffer and then outputs the lot with err_fwrite.  In testing, the
new code was slightly faster than the old version, with the added benefit
that it will stop promptly if IO problems are detected.
 		2013-01-09 14:43:36 +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 Added wrappers for fputc and fputs; more efficient sequence printing 2013-01-09 14:43:36 +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 Added wrappers for fputc and fputs; more efficient sequence printing 2013-01-09 14:43:36 +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 Added wrappers for fputc and fputs; more efficient sequence printing 2013-01-09 14:43:36 +00:00
utils.h Added wrappers for fputc and fputs; more efficient sequence printing 2013-01-09 14:43:36 +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