e43eace9e5
Update bwa.1
2022-02-18 13:36:09 -08:00
9f26bfcc77
Released bwa-0.7.17 (r1188)
2017-10-23 13:10:17 -04:00
47d9fb27d7
Release 0.7.16-r1180
2017-07-30 22:35:38 -04:00
83260ccb10
Merge pull request #60 from jdagilliland/typo
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Typos, doc improvements in man page
2017-07-30 18:59:11 -04:00
0976272d99
Merge pull request #139 from jmarshall/fixes
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Various collected fixes (updated versions of several existing PRs)
2017-07-30 18:36:07 -04:00
bc58bf265d
Add "bwa mem -o FILE" synonym and documentation
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As -o is still free in the mem command, use that standard option to
specify an output file (and keep -f to parallel bwase/bwape commands).
Document it in the usage and man page.
2017-06-27 17:05:44 +01:00
08764215c6
Merge branch 'dev'
2016-05-31 09:43:16 -04:00
850dd811fc
Release bwa-0.7.15-r1140
2016-05-31 09:42:50 -04:00
d6636daead
Include in man page info on read types
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Previously this info had only been present in the help text emitted from
`bwa mem` without arguments, but I think it helpful to include in man page.
2016-03-31 12:40:09 -04:00
e10fc577e1
Fix a few typos in man page
2016-03-31 12:40:03 -04:00
6460ef5572
Minor doc fix
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MAN page described `bwa mem` option `-D` variously as integer and float,
when it is in fact a float.
2016-03-17 12:00:47 -04:00
be2020c4af
ropebwt2 for bwt construction
2016-01-26 13:46:08 -05:00
8211fbcb62
Released 0.7.12
2014-12-28 15:44:59 -05:00
408fd5e072
Released bwa-0.7.11-r1034
2014-12-23 15:29:18 -05:00
ed95769a33
updated documentations
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(prepare for release)
2014-12-21 16:30:29 -05:00
61ab329639
fine tune the wrapper scripts
2014-11-18 15:40:58 -05:00
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
a35a6c2580
updated maual page
2014-05-12 12:52:16 -04:00
39a6cd5bb0
r762: cleanup for the new release; unfinished
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It will take to make the documentation ready.
2014-05-11 15:15:44 -04:00
3efb7c0e91
r455: release bwa-0.7.8
2014-03-31 15:27:23 -04:00
417c6d66c7
dev-r451: fixed a few bugs when -A!=1
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Something is still wrong.
2014-03-31 10:52:45 -04:00
1c19bc630f
Released bwa-0.7.7-r441
2014-02-25 01:05:37 -05:00
5fdab3ae13
Released bwa-0.7.6-r432
2014-01-31 11:12:59 -05:00
607e11d43d
updated README
2013-05-24 20:49:36 -04:00
c14aaad1ce
Released bwa-0.7.4-r385
2013-04-23 11:40:56 -04:00
2087dc162f
r377: increased unpaired penalty from 9 to 17
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This leads to more aggressive pairing - more properly paired reads. I have
found a few cases where, for example, read1 is umambiguously mapped to chr20
while its 100bp mate has a perfect match to another chr but has 3 mismatches
and 1 deletion when it is paired with read1 on chr20. With longer reads, it
seems that the chr20 hit is correct, although it is not obvious how this
happened in evolution.
2013-04-17 16:50:20 -04:00
9346acde1b
Release bwa-0.7.3a-r367
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In 0.7.3, the wrong CIGAR bug was only fixed in one scenario, but not fixed
in another corner case.
2013-03-15 21:26:37 -04:00
7dec00c217
Release BWA-0.7.3-r366
2013-03-15 12:51:53 -04:00
bdf34f6ce7
r363: XA=>XP; output mapQ in XP
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In BWA, XA gives hits "shadowed" by the primary hit. In BWA-MEM, we output
primary hits only. Primary hits may have non-zero mapping quality.
2013-03-12 09:56:04 -04:00
5581cb9152
Release bwa-0.7.2-r351
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For the TLEN sign fix. Sorry for the significant bug in 0.7.0/0.7.1
2013-03-09 18:15:41 -05:00
2d01a297fb
Improving 'properly paired' flag.
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If one end has a low quality tail that happens to have a score-20 hit,
the pair won't be flagged as properly paired because bwa-mem thought it has
multiple hits. By filtering with -T, we won't have this problem.
2013-03-09 18:05:50 -05:00
1d132a546d
Release 0.7.1-r347
2013-03-08 15:30:06 -05:00
b0a76884e8
r340: feature freeze; updated the manpage
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I will stop adding new features to bwa and prepare for the next release. I will
briefly evaluate the variant calling accuracy before the release.
2013-03-07 11:51:23 -05:00
4bb0bdddca
r306: introduce clipping penalty
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More clipping leads to more severe reference bias. We should not clip the
alignment unless necessary.
2013-02-27 21:13:39 -05:00
292e92b602
r303: bugfix - wrong band width when CIGAR
2013-02-27 15:39:15 -05:00
e620f0ff4e
r302: updated the manpage
2013-02-27 13:16:22 -05:00
09ee115dcc
r126: release bwa-0.6.2
2012-06-19 13:29:44 -04:00
91a4a0c8ea
Release bwa-0.6.1
2011-11-28 09:52:07 -05:00
dec584d50b
fixed a long-existing bug in trimming
2011-11-23 23:11:50 -05:00
f1517b845c
updated manual
2011-11-12 18:35:04 -05:00
1f970b4557
updated revision number
2011-10-24 14:14:42 -04:00
87664941b0
Release bwa-0.5.9 (r16)
2011-01-24 22:00:24 -05:00
0380cf02bf
update the manual page
2011-01-18 23:27:55 -05:00
5e30884730
Update to the latest modfication 0.5.9rc1-2. Update ChangeLog
2011-01-13 20:54:10 -05:00
007c3eb75d
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
Nils Homer
Heng Li
John Marshall
Jason Gilliland
Heng Li