666638a953
changed the default scoring
2013-02-04 14:51:51 -05:00
ba18db1a9f
sw extension works for the simplest case
2013-02-04 12:37:38 -05:00
f83dea36d8
no effective changes
2013-02-03 18:16:43 -05:00
2093398231
bugfix: the first line is wrong
2013-02-03 17:47:57 -05:00
e8a1962efe
code backup; it is wrong
2013-02-03 17:25:40 -05:00
92b084e553
reimplemented SW extension; not tested yet
2013-02-02 16:38:21 -05:00
d25a87cc50
code backup
2013-02-02 15:14:24 -05:00
00e5302219
routine to get subsequence from 2-bit pac
2013-02-01 16:39:50 -05:00
7ab4b3321f
bugfix: memory leak
2013-02-01 15:26:34 -05:00
f8f3b7577a
code cleanup; added a missing file
2013-02-01 14:38:44 -05:00
620ad6e5b9
reseed long SMEMs
2013-02-01 14:20:38 -05:00
abc675f278
typo in comments
2013-02-01 13:14:16 -05:00
86f2e134ba
no effective changes
2013-02-01 12:57:48 -05:00
5d372cef65
bugfix: wrong B-tree comparison
2013-01-31 16:39:24 -05:00
8977737460
basic chaining working
...
Definitely suboptimal in a lot of corner cases...
2013-01-31 16:26:05 -05:00
6c19c9640c
code backup
2013-01-31 15:55:22 -05:00
91debf412b
move smem iterators to bwamem.{c,h}
2013-01-31 13:59:48 -05:00
5a4a0c4173
a bit refactoring for further changes
2013-01-31 12:34:05 -05:00
6de74888fd
bugfix: min_intv not working in SMEM
2013-01-31 12:12:58 -05:00
543c719a54
fixed a couple of unimportant bugs in SMEM
2013-01-31 11:53:07 -05:00
6641788d38
preparation for further changes
2013-01-31 11:42:31 -05:00
292f9061ab
r132: optionally copy FASTA/Q comment to SAM
2012-10-26 12:54:32 -04:00
3abfd0743a
r131: r128 plus remote changes
2012-06-28 14:52:18 -04:00
fa51f029b9
Merge branch 'master' of github.com:lh3/bwa
2012-06-28 14:51:51 -04:00
f44edd4fc9
r128: more conservative chaining filter
2012-06-28 14:51:02 -04:00
0ae318be0d
resolve duphits after right extension as well
2012-06-28 13:32:58 -04:00
f89649ee26
Merge pull request #11 from sjackman/inline
...
Do not inline functions used externally
2012-06-26 07:02:49 -07:00
84d34e1d0b
Do not inline functions used externally
...
Compiling using CLANG gives the following errors:
Undefined symbols for architecture x86_64:
"_bwt_occ", referenced from:
_bwt_cal_sa in bwt.o
_bwt_sa in bwt.o
"_bwt_2occ", referenced from:
_bwt_match_exact in bwt.o
_bwt_match_exact_alt in bwt.o
_bwt_cal_width in bwtaln.o
"_bwt_2occ4", referenced from:
_bwt_match_gap in bwtgap.o
_bsw2_core in bwtsw2_core.o
"_bwtl_2occ4", referenced from:
_bsw2_core in bwtsw2_core.o
2012-06-25 12:48:43 -07:00
09ee115dcc
r126: release bwa-0.6.2
2012-06-19 13:29:44 -04:00
29ed2d8287
rename the "api" branch as "master"
2012-06-19 13:13:29 -04:00
d97ff6bf72
r124: updated version number
2012-04-17 20:45:07 -04:00
72f1a95448
Merge branch 'master' into api
2012-04-17 20:44:30 -04:00
cd818687ac
r115: added -I and -S to bwasw
2012-04-17 20:43:43 -04:00
4f61e2b7f5
unnecessary large .sai output
2012-04-17 19:31:37 -04:00
9c486fa41e
updated APIs abit
2012-04-08 00:55:52 -04:00
3b5a9e5595
simplified bwa_se() interface
2012-04-08 00:12:34 -04:00
ca93a71e6e
complete single-end alignment
2012-04-08 00:02:06 -04:00
080726cb47
preliminary doc
2012-04-07 22:50:07 -04:00
1cef219667
compute CIGAR; rev seq not working
2012-04-07 22:00:03 -04:00
66154ff5d2
towards refined gapped; unfinished
2012-04-07 01:25:39 -04:00
a1abfe9977
API: aln seems working
2012-04-07 00:23:01 -04:00
cff473393c
commented out debugging code
2012-04-02 12:05:15 -04:00
790df95e1a
updated revision number
2012-04-02 11:43:32 -04:00
36f2fd6238
bugfix: incorrect bandwidth
2012-04-02 11:39:40 -04:00
d3169804f6
debugging; bug persistant
2012-04-02 10:45:42 -04:00
173b93dfd4
debugging code: bwasw has a rare bug
2012-04-02 09:37:02 -04:00
d33abf127f
check *.64.bwt first and then *.bwt
2012-03-29 14:45:00 -04:00
c875085b2b
do not use .64 suffix by default
2012-03-29 12:31:01 -04:00
bdc953cad9
Tim's suggestion suffix file name with .64
2012-03-29 12:22:51 -04:00
a471f1918b
bugfix: long-existing out-of-boundary bug
2012-03-19 13:45:09 -04:00
Heng Li
Heng Li
Shaun Jackman