.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
Fixing problem with linking to libm on some Ubuntu systems (I see this on machine running 11.04, kernel 3.0.0-14-virtual). Changing order of -lm on the command line seems to do the trick and should be tolerated in other environments.
2013-03-05 20:48:16 +00:00
NEWS
r313: release bwa-0.7.0
2013-02-28 15:56:05 -05:00
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
r316: don't allocate zero-length memory
2013-03-04 10:22:18 -05:00
bntseq.h
r283: prepare for fixing cross-ref aln
2013-02-25 22:49:15 -05:00
bwa.1
r306: introduce clipping penalty
2013-02-27 21:13:39 -05:00
bwa.c
move mem_fill_scmat() to bwa.{h,c}
2013-03-05 09:38:12 -05:00
bwa.h
move mem_fill_scmat() to bwa.{h,c}
2013-03-05 09:38:12 -05:00
bwamem.c
r332: added output threshold
2013-03-05 22:49:38 -05:00
bwamem.h
r332: added output threshold
2013-03-05 22:49:38 -05:00
bwamem_pair.c
r284: amend cross-reference hit
2013-02-26 00:03:49 -05:00
bwape.c
r329: ditch stdaln.{c,h}; no changes to bwa-mem
2013-03-05 12:00:24 -05:00
bwase.c
r331: rewrote CIGAR generation for bwa-short
2013-03-05 19:56:37 -05:00
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
cleanup bwt_occ()
2013-02-26 12:09:28 -05:00
bwt.h
move bwt_invPsi() from bwt.h to bwt.c
2013-02-26 11:57:36 -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
merged bwtmisc.c to bwtindex.c
2013-02-22 17:23:34 -05:00
bwtsw2.h
r132: optionally copy FASTA/Q comment to SAM
2012-10-26 12:54:32 -04:00
bwtsw2_aux.c
bwa-sw: ditch stdaln
2013-03-05 10:12:38 -05:00
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
r314: cleanup bwamem API
2013-03-01 11:14:51 -05:00
fastmap.c
r332: added output threshold
2013-03-05 22:49:38 -05:00
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
separated and improved SAM printing code
2013-02-11 15:29:03 -05:00
ksw.c
bwa-sw: ditch stdaln
2013-03-05 10:12:38 -05:00
ksw.h
r323: added Z-dropoff, a variant of blast's X-drop
2013-03-05 00:34:33 -05:00
kvec.h
generate multiple alignments from one chain
2013-02-21 14:58:51 -05:00
main.c
r332: added output threshold
2013-03-05 22:49:38 -05:00
main.h
removed another part related to color-space
2013-02-22 17:15:57 -05:00
pemerge.c
De-overlap paired-end reads
2013-03-06 19:23:45 -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
773b86331b