.gitignore
to exclude "test64"
2013-02-12 10:39:16 -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
r342: bugfix in bwasw - AS is off by one
2013-03-08 12:06:45 -05:00
NEWS
Release bwa-0.7.3a-r367
2013-03-15 21:26:37 -04:00
QSufSort.c
removed a few unused variables
2013-02-23 13:26:50 -05:00
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
r334: added pemerge to bwa
2013-03-06 21:55:02 -05:00
bntseq.h
r283: prepare for fixing cross-ref aln
2013-02-25 22:49:15 -05:00
bwa.1
Release bwa-0.7.3a-r367
2013-03-15 21:26:37 -04:00
bwa.c
r368: bugfix - wrong CIGAR when bridging 3 contigs
2013-03-18 20:49:32 -04:00
bwa.h
move mem_fill_scmat() to bwa.{h,c}
2013-03-05 09:38:12 -05:00
bwamem.c
r376: reduce wasteful seed extension
2013-04-10 12:18:56 -04:00
bwamem.h
r373: optionally distable mate rescue
2013-04-09 16:13:55 -04:00
bwamem_pair.c
r373: optionally distable mate rescue
2013-04-09 16:13:55 -04:00
bwape.c
r329: ditch stdaln.{c,h}; no changes to bwa-mem
2013-03-05 12:00:24 -05:00
bwase.c
r375: fixed compiling errors by the last change
2013-04-10 11:04:32 -04:00
bwase.h
removed color-space support
2013-02-12 10:21:17 -05:00
bwaseqio.c
updated to the latest kseq.h
2013-02-06 14:38:40 -05:00
bwt.c
fixed an issue caused by a Mac/Darwin bug
2013-04-09 15:17:04 -04:00
bwt.h
Updated NEWS; added stddef.h for size_t
2013-03-08 14:14:42 -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
r329: ditch stdaln.{c,h}; no changes to bwa-mem
2013-03-05 12:00:24 -05:00
bwtaln.h
r329: ditch stdaln.{c,h}; no changes to bwa-mem
2013-03-05 12:00:24 -05:00
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
r335: fixed a compiling error
2013-03-06 21:57:13 -05:00
bwtsw2.h
r132: optionally copy FASTA/Q comment to SAM
2012-10-26 12:54:32 -04:00
bwtsw2_aux.c
r375: fixed compiling errors by the last change
2013-04-10 11:04:32 -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
cleanup index loading code
2013-02-23 16:10:48 -05:00
bwtsw2_pair.c
prepare to ditch stdaln.{h,c}
2013-03-04 10:32:33 -05:00
example.c
r359: identical output to 0.7.2 (without -a)
2013-03-11 23:16:18 -04:00
fastmap.c
r373: optionally distable mate rescue
2013-04-09 16:13:55 -04:00
is.c
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
kbtree.h
code cleanup; added a missing file
2013-02-01 14:38:44 -05:00
khash.h
Multiple changes:
2013-02-12 09:50:28 -05:00
kopen.c
cleanup bwt_occ()
2013-02-26 12:09:28 -05:00
kseq.h
updated to the latest kseq.h
2013-02-06 14:38:40 -05:00
ksort.h
code backup
2013-02-12 09:22:47 -05:00
kstring.c
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
kstring.h
prepare to replace the SAM printing code
2013-03-11 21:25:17 -04:00
ksw.c
r374: fix - clipping penalty not always working
2013-04-10 01:09:37 -04:00
ksw.h
r374: fix - clipping penalty not always working
2013-04-10 01:09:37 -04:00
kvec.h
generate multiple alignments from one chain
2013-02-21 14:58:51 -05:00
main.c
r376: reduce wasteful seed extension
2013-04-10 12:18:56 -04:00
pemerge.c
r339: pemerge - expose some settings to CLI
2013-03-07 11:22:19 -05:00
qualfa2fq.pl
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
utils.c
moved some common code to bwa.{c,h}
2013-02-23 15:30:46 -05:00
utils.h
moved some common code to bwa.{c,h}
2013-02-23 15:30:46 -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
499cf4c00d