624687b072
r829: killed a harmless gcc warning
2014-09-15 23:33:22 -04:00
5d26ab0ee3
r828: changed the default scoring for pacbio
2014-09-15 23:22:05 -04:00
b07587f806
r827: an alt hit as good as a pri hit as supp
2014-09-15 16:07:51 -04:00
bd85af08ab
r826: improved alt mapping for PE
2014-09-15 12:13:04 -04:00
aee53f1334
r824: ALT mapping seems working
2014-09-15 00:29:05 -04:00
015ab3f6c3
r823: towards ALT support
2014-09-14 16:41:14 -04:00
8116bcc786
Merge branch 'dev' into alt
2014-09-14 15:40:52 -04:00
8d2b93156b
r821: more relax on containing seeds
2014-09-12 10:35:49 -04:00
6739b713dd
Merge branch 'hotfix-utgaln' into dev
...
Conflicts:
main.c
2014-09-08 12:44:42 -04:00
f4aedddee6
r819: bugfix - added too many sub-SMEMs
2014-09-08 11:32:48 -04:00
ca61fe3ad5
code backup
2014-09-08 08:52:02 -04:00
1934f0cf24
code backup
2014-09-05 13:20:52 -04:00
e4ad616d43
r816: read .alt file (not tested)
2014-09-05 12:49:50 -04:00
35ac99b4f7
r815: optionally output ref fasta header
...
Also fixed a bug in reading .ann files
2014-08-29 10:51:23 -04:00
1e611b235c
r810: add err_puts()
...
puts() adds '\n', but fputs() does not.
2014-08-26 11:07:24 -04:00
b5cba257c1
r809: new strategy for the -a mode
2014-08-25 11:59:27 -04:00
bf7d1d46ca
r808: a minor bug with the new index -b
2014-08-25 10:36:24 -04:00
1bba5ef20e
r807: allow to change block size in bwt_gen
...
For a very large reference genome, the default is too small.
2014-08-25 10:31:54 -04:00
b73f4c977a
Merge branch 'master' into new-master
2014-08-07 21:51:58 -04:00
0a6f2660b4
Fixed a bug related to the score returned.
2014-08-07 13:50:42 -07:00
c1df343740
Merge branch 'master' of github.com:lh3/bwa
2014-08-07 13:49:01 -07:00
9bdcf31dec
don't process hard clipped SEQ
...
The full read sequence has to be present.
2014-08-07 13:48:51 -07:00
a1a57d97be
r796: more debugging code
2014-08-07 14:58:51 -04:00
d9dfab2ba2
r795: intel's ksw_extend() replacement
2014-08-07 13:43:07 -04:00
b5415ba23d
first integration; compiled, but NOT TESTED!
2014-08-07 11:59:37 -04:00
5e56bec0f4
don't process hard clipped SEQ
...
The full read sequence has to be present.
2014-08-07 10:36:28 -04:00
705aa53894
Released 0.7.10
2014-07-13 22:57:27 -04:00
7fd6a11569
r788: segfault when the last ref is "weird"
...
mem_patch_reg() did not check if two hits are on the same strand, which may
lead to an alignment bridging the forward-backward boundary.
2014-07-10 10:53:56 -04:00
cffff4338f
r787: use mem_seed_sw() also for non-PacBio reads
...
In the previous version, mem_seed_sw() is only used for PacBio reads to filter
bad seeds. For non-PacBio long queries, bwa-mem uses mem_chain2aln_short() for
a similar purpose. However, it turns out that mem_chain2aln_short() is not
effective given long near-tandem repeats. Bwa-mem still wastes a lot of time
of futile ref substring and extensions.
In this commit, mem_chain2aln_short() has been removed. mem_seed_sw() is used
if the query sequence is long enough (~700bp). For shorter reads, the results
should be almost identical to the previous version.
2014-07-10 10:30:22 -04:00
3efc33160c
0.7.9a-r786: fixed a segfault in a rare case
...
More likely to happen given a circular genome
2014-05-19 16:47:25 -04:00
031d3d83ce
Wrong release number: 0.7.8 => 0.7.9
2014-05-19 09:49:26 -04:00
be74dbc00c
Release bwa-0.7.9-r783
2014-05-19 09:09:11 -04:00
e4752b321b
Release bwa-0.7.9-r782
2014-05-19 09:08:07 -04:00
f00cc94e1d
r779: fixed a memory leak in SE
2014-05-16 00:06:34 -04:00
a5ad0cff7f
r778: reduced the number of alloc() calls a bit
2014-05-15 23:23:04 -04:00
012d54fc49
Updated release notes
2014-05-15 11:48:28 -04:00
8d2986ece2
r770: fixed a compiling warning
2014-05-14 14:44:03 -04:00
8f3e7d573b
fixed wrong FAQ links
2014-05-14 14:36:52 -04:00
d67e923026
changed the heading format
2014-05-14 14:33:42 -04:00
1627f9dfae
updated README
2014-05-14 14:32:09 -04:00
061c63f36a
r766: removed useless code
2014-05-13 13:09:29 -04:00
0168f39eeb
r765: fixed a declaration error
...
Reported by Andreas Tile from Debian
2014-05-13 12:54:23 -04:00
08517ac09b
r764: changed -c in "-x pacbio" to 500
2014-05-13 12:53:24 -04:00
a35a6c2580
updated maual page
2014-05-12 12:52:16 -04:00
39a6cd5bb0
r762: cleanup for the new release; unfinished
...
It will take to make the documentation ready.
2014-05-11 15:15:44 -04:00
cfe6996173
r760: removed commented code
...
It is slow and is not very effective. And I hate useless code.
2014-05-09 14:59:07 -04:00
43b498a37e
r759: bugfix - frac_rep not working
...
Also added commented code for a 3rd round seeding. Not used.
2014-05-09 14:56:59 -04:00
c9b33502f3
r758: fixed a typo
...
mostly negligible in practice
2014-05-07 15:07:29 -04:00
e56572e88f
help on how to use bwa-helper.js
2014-05-06 17:11:17 -04:00
1ced2f386c
more debugging info at -v5
2014-05-06 16:35:40 -04:00
Heng Li
Mustafa Ozdal