030825ae85
updated release notes
2014-09-18 11:51:52 -04:00
ba7ed47d40
error in altpost
2014-09-18 11:18:10 -04:00
a41afe4c97
These files were committed on a wrong branch
2014-09-18 10:49:35 -04:00
a32d44d8d6
r855: show ALT hits in the PE mode, too
...
In the previous version, it does not
2014-09-17 23:07:56 -04:00
c982443210
r854: improved the calculation of pa
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and build pa filtering into BWA-MEM
2014-09-17 16:26:28 -04:00
f5a0e576e6
added postalt to bwa-helper for post processing
2014-09-17 14:18:40 -04:00
825ae92e58
r849: the pa tag now gives a number
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... which is the ratio of this hit to the best ALT hit.
2014-09-17 13:05:35 -04:00
6f37c14f26
r848: tag alignments with primary ALT
2014-09-16 18:52:49 -04:00
a458442b24
r845: updated NEWS
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I will use the new version for a while and then release it.
2014-09-16 14:38:41 -04:00
92bc6849a3
r844: added intra-species contig mapping mode
2014-09-16 10:53:07 -04:00
90518f11e3
r843: presetting for ONT 2d reads
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Somewhat working for 1d reads, but not very well
2014-09-16 10:38:15 -04:00
230cd16712
updated dependency
2014-09-16 10:17:30 -04:00
d0af3648d1
Fixed a typo
2014-09-16 10:16:45 -04:00
43ce69104d
Removed PacBio read-to-read instruction
2014-09-15 23:59:35 -04:00
d013ea94b0
Removed instruction on ALT alignment
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Favoring the new method
2014-09-15 23:45:17 -04:00
4b6eeb34c8
r830: optionally fixed chunk size
2014-09-15 23:42:24 -04:00
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
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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
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Also fixed a bug in reading .ann files
2014-08-29 10:51:23 -04:00
1e611b235c
r810: add err_puts()
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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
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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
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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"
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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
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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
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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
Heng Li
Mustafa Ozdal