a03d01f944
r878: XA is given to the best alignment
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Non-ALT hits may get ALT hits in the XA tag. This will simplify haplotype
assignment.
2014-09-30 13:50:51 -04:00
dae4ca3ced
r875: invalid SAM output for ALT hits
2014-09-26 15:29:08 -04:00
7426a750ec
r868: use soft clip for ALT hits
2014-09-19 16:58:18 -04:00
9af36064e8
r867: fixed a few bugs; added ALT hits to XA
2014-09-19 16:50:21 -04:00
a41afe4c97
These files were committed on a wrong branch
2014-09-18 10:49:35 -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
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
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
b07587f806
r827: an alt hit as good as a pri hit as supp
2014-09-15 16:07:51 -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
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
b5cba257c1
r809: new strategy for the -a mode
2014-08-25 11:59:27 -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
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
061c63f36a
r766: removed useless code
2014-05-13 13:09:29 -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
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
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
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
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
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
b603fed39c
r733: bugfix - seed score unset when no -W
2014-04-29 14:58:53 -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
Heng Li