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
8d2986ece2
r770: fixed a compiling warning
2014-05-14 14:44:03 -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
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
6ac8dd5840
r754: added command msg for -h
2014-05-06 16:15:14 -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
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
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
45f24b4ae8
r720: improved overlap hit merging
2014-04-15 16:09:42 -04:00
bdb7b000cd
r719: more stringent overlap merge
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Will consider to make it the default
2014-04-15 14:52:17 -04:00
4e22270eba
r718: merge alnregs overlapping on both query/ref
2014-04-14 17:01:17 -04:00
6d4a6debdc
r716: changed -x pbread
2014-04-14 16:04:29 -04:00
bbcabfe342
r707: change params for pacbio-to-pacbio
2014-04-10 21:53:52 -04:00
658f27eae4
Merge branch 'dev' into layout
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Conflicts:
main.c
2014-04-10 21:48:47 -04:00
6fda93502f
r705: pairing performed on one chr only
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Change of versioning: the revision number is acquired with:
git rev-list --all --count
This counts the total number of commits across all branches.
2014-04-10 21:38:14 -04:00
db4b171fa6
Merge branch 'dev' into layout
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Conflicts:
main.c
2014-04-10 21:09:47 -04:00
07182d9061
dev-475: -F outputs unit score, not raw score
2014-04-10 21:09:06 -04:00
7d25fe2de3
Merge branch 'dev' into layout
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Conflicts:
main.c
2014-04-10 21:07:16 -04:00
e80bccc923
dev-474: fixed a typo
2014-04-10 21:04:02 -04:00
f02cd42679
dev-473: added a few assertions
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to make sure the new change works as is expected
2014-04-10 21:03:13 -04:00
8638cfadc8
dev-472: get rid of bwa_fix_xref()
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This function causes all kinds of problems when the reference genome consists
of many short reads/contigs/chromsomes. Some of the problems are nearly
unfixable at the point where bwa_fix_xref() gets called. This commit attempts
to fix the problem at the root. It disallows chains spanning multiple contigs
and never retrieves sequences bridging two adjacent contigs. Thus all the
chaining, extension, SW and global alignments are confined to on contig only.
This commit brings many changes. I have tested it on a couple examples
including Peter Field's PacBio example. It works well so far.
2014-04-10 20:54:27 -04:00
e2d0c996e9
layout-477: output unit score, not the raw score
2014-04-10 18:03:28 -04:00
Heng Li