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基于bwa，做一些优化，注释
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Rob Davies 752ce69b78 Added more wrappers for functions that make system calls 
Added the following wrappers that check the results of system calls
and exit non-zero if something went wrong.  This is so bwa can be more
robust against system failures (e.g. IO errors from remote storage, or
running out of memory).  The existing and new wrappers have also been
modified so that they no longer try to dump core on failure.  In most cases
the resulting core files are not useful (especially if bwa was compiled
with optimization turned on) so just pollute whatever directories they
got written to.

Wrappers for memory allocation functions:

xcalloc
xmalloc
xrealloc
xstrdup

New wrappers for IO functions:

err_fread_noeof   (also dies on EOF)
err_gzread
err_fseek
err_rewind
err_ftell
 		2012-12-16 10:05:32 +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 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 r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -04:00
bwtsw2_aux.c r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -04:00
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 r132: optionally copy FASTA/Q comment to SAM 2012-10-26 12:54:32 -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 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 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 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