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
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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
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It will take to make the documentation ready.
2014-05-11 15:15:44 -04:00
cfe6996173
r760: removed commented code
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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
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Also added commented code for a 3rd round seeding. Not used.
2014-05-09 14:56:59 -04:00
c9b33502f3
r758: fixed a typo
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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
4b951592fb
download link of data used by genalt
2014-05-06 16:29:20 -04:00
6ac8dd5840
r754: added command msg for -h
2014-05-06 16:15:14 -04:00
81970e7687
more comments
2014-05-06 16:12:22 -04:00
c50ee8c841
genalt is working
2014-05-06 16:02:40 -04:00
8d37726325
code backup
2014-05-06 11:57:02 -04:00
024195db62
code backup
2014-05-05 16:51:14 -04:00
ce3c198245
r749: max_hits tunable on CMD; default to 5
2014-05-04 10:17:03 -04:00
f21d6498bc
r748: reduced the default -m to 50
2014-05-02 16:49:19 -04:00
e8f28cb529
r747: fixed a minor issue in the last (mis)commit
2014-05-02 16:17:50 -04:00
6db761e269
r746: tuned heuristic for GRCh38
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Reduced -c to 500 by default. As a compensation, we choose up to 1000 positions
if a seed has 500 or more occurrences. In addition, a read with big portion
from such seeds will have lower mapping quality.
2014-05-02 16:06:27 -04:00
8763e0ced7
Helpful scripts
2014-05-02 10:43:49 -04:00
b7076848ab
r744: int overflow given MB query
2014-05-01 15:30:36 -04:00
fa20c71920
r742: further control the max bandwidth
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I am looking at 6kb bandwidth...
2014-05-01 14:27:38 -04:00
7954e77a1b
r741: fixed segfault in rare cases
2014-05-01 11:13:05 -04:00
4b2441069f
r740: don't attempt merge if bandwidth too large
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Sometimes the bandwidth can be >10k.
2014-05-01 11:01:52 -04:00
5aedc978d1
r739: output suboptimal hits in the PE mode
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However, PE information is not used for suboptimal hits
2014-04-30 23:23:54 -04:00
c6c943f9d7
r738: output multi-map in the XA tag (SE only)
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... PE support coming soon
2014-04-30 16:46:05 -04:00
d59d78838c
r737: fixed an assertion when failed to convert sa
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A bug pointed out by Mikkle Schubert
2014-04-30 14:55:44 -04:00
88f89be60e
r736: improved in low-complexity regions
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Example: GGAGGGGAAGGGTGGGCTGGAGGGGACGGGTGGGCTGGAGGGGAAGGGTGTGCTGGAGGGAAAAGGTGGACTGGAGGGGAAGGGTGGGCTGGAGGGGAAGG
This read has 5 chains, two of which are:
weight=80 26;26;0,4591439948(10:-3095894) 23;23;27,4591439957(10:-3095888) 31;31;70,4591439964(10:-3095873)
weight=50 45;45;51,4591440017(10:-3095806) 50;50;51,4591440017(10:-3095801) 31;31;70,4591440090(10:-3095747)
Extension from the 26bp seed in the 1st chain gives an alignment [0,101) <=> [4591439948,4591440067), which
contains the 50bp seed in the second chain. However, if we extend the 50bp seed, it yields a better alignment
[0,101) <=> [4591439966,4591440067) with a different starting position. The 26bp seed is wrong. This commit
adds a heuristic to fix this issue.
2014-04-30 14:14:20 -04:00
11698fc4e5
r735: fixed a bug caused by merge
2014-04-30 13:12:43 -04:00
b603fed39c
r733: bugfix - seed score unset when no -W
2014-04-29 14:58:53 -04:00
44754cd615
r731: separate layouter
2014-04-28 10:39:29 -04:00
dadd5d6281
r730: more permissive about merging overlapping
2014-04-28 10:01:54 -04:00
76bb49e01b
r729: halved band width; doubled patch band width
2014-04-24 16:06:01 -04:00
6052d3015b
r728: sorting the end in mem_sort_dedup_patch()
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The older version does this, which is correct.
2014-04-24 15:44:59 -04:00
df65893fb5
r727: extend seeds with SW
2014-04-24 14:28:40 -04:00
b92bbb47e5
Merge branch '0.7.7-softclip' into layout
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Conflicts:
Makefile
bwamem.h
fastmap.c
main.c
2014-04-24 12:24:49 -04:00
8c12ec4a4b
r725: optionally disable hard clipping
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as is reqested by the cancer group
2014-04-24 11:56:43 -04:00
954cfd766d
improved ksw_extend2()
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1. the first cell in a row is not always right
2. prevent from H->H extension from H=0 cells
3. replaced the band narrowing heuristic with always correct one
2014-04-23 15:14:52 -04:00
b93fca2b2e
r723: merge adjacent hits
2014-04-16 16:38:50 -04:00
48847af2fc
code backup
2014-04-16 12:00:13 -04:00
00a07f61bf
r721: merge overlapping hits by default
2014-04-15 16:16:04 -04:00
Heng Li