a09db69037
In bwtsw, replace the batch seq-reader with bseq
2013-02-06 17:12:27 -05:00
901d28d5f5
code backup
2013-02-06 15:03:09 -05:00
5a0b32bfd2
updated to the latest kseq.h
2013-02-06 14:38:40 -05:00
a9292d674d
a bit code cleanup
2013-02-06 13:59:32 -05:00
e65b2096f7
removed useless members
2013-02-06 12:25:49 -05:00
797a8c147e
sorting chains while filtering chains
2013-02-05 21:58:33 -05:00
a61288c768
separate CIGAR generation
2013-02-05 21:49:19 -05:00
14e6a7bdb9
fixed a silly bug in ksw_extend()
...
Query return value is assigned to the target variable and vice versa...
2013-02-05 17:29:03 -05:00
1e16f3e701
calling ksw_global(); ksw_extend() is buggy!
2013-02-05 17:13:12 -05:00
86caae811e
added comments
2013-02-05 16:58:35 -05:00
1bc9712cd8
explicitly use bit to keep bt matrix
...
This also simplifies backtracking.
2013-02-05 16:28:15 -05:00
7e1466c885
implemented NW backtrack
2013-02-05 16:05:53 -05:00
d91e320972
towards reimplementing banded NW alignment
2013-02-05 12:06:56 -05:00
7067af833d
fixed a silly bug on sorted merge
2013-02-05 00:41:07 -05:00
d6a73c9171
chain filtering apparently working
2013-02-05 00:17:20 -05:00
9d0cdb2d3c
unfinished chain filter
2013-02-04 17:23:06 -05:00
c589b42fb5
minor tuning for fewer identical hits
2013-02-04 16:48:11 -05:00
29c8546679
better ref extraction
2013-02-04 16:08:00 -05:00
788e9d1e3d
fixed a couple of leaks; buggy atm
2013-02-04 15:40:26 -05:00
f27bd18f20
check if every seed is included; not used for now
2013-02-04 15:09:47 -05:00
5bfa45a69b
write the mem_aln_t struct
2013-02-04 15:02:56 -05:00
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
Heng Li
Heng Li
Shaun Jackman