4cb5110d03
Merge branch 'master' into master_fixes
2013-04-22 09:51:07 +01:00
f6ae0d4d0f
r382: similar treatment in bwa-sw (see r381)
2013-04-19 17:52:06 -04:00
3f8caef33c
r381: fixed a bug when upper bound < max read len
2013-04-19 17:44:35 -04:00
db7a98636f
r380: er... another compiling error
2013-04-19 12:04:44 -04:00
f0c94d80d1
r379: fixed compiling error
2013-04-19 12:04:00 -04:00
be11e27e12
r378: bugfix - wrong CIGAR
...
This is actually caused by a bug in SSE2-SW, where the query begin may be
smaller than the true one if there is an exact tandem repeat.
2013-04-19 12:00:37 -04:00
2087dc162f
r377: increased unpaired penalty from 9 to 17
...
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
3dd10bd7db
Merge branch 'master' into master_fixes
2013-04-12 16:20:13 +01:00
90ecd344ba
Merge branch 'master' into master_fixes. Merged up to master r375.
...
Conflicts:
bwt.c
2013-04-11 11:15:39 +01:00
499cf4c00d
r376: reduce wasteful seed extension
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mainly for contig alignment
2013-04-10 12:18:56 -04:00
47520134e7
r375: fixed compiling errors by the last change
2013-04-10 11:04:32 -04:00
3d8a8c1e37
r374: fix - clipping penalty not always working
...
This only happens to gaps where mem underestimates the bandwidth without
considering the clipping penalty.
2013-04-10 01:09:37 -04:00
53bb846407
r373: optionally distable mate rescue
2013-04-09 16:13:55 -04:00
d64eaa851d
fixed an issue caused by a Mac/Darwin bug
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On Mac/Darwin, it is not possible to read >2GB data with one fread().
2013-04-09 15:17:04 -04:00
d7ca0885eb
r371: extend overlapping seeds
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to avoid misalignment in tandem repeats
2013-04-04 00:43:43 -04:00
1e118e0823
r370: suppress "D" at the end of a cigar
...
This is caused by seeds in tandem repeats, in which case, bwa-mem may not
extend the true seed. The change in this commit is only a temporary cure.
2013-04-03 23:57:19 -04:00
c89756e2b0
Merge branch 'master' into master_fixes
2013-03-19 12:11:51 +00:00
8437cd4edd
r369: bugfix - segfault caused by the last change
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Sigh... Even the simplest change can lead to new bugs.
2013-03-19 01:04:57 -04:00
1e3cadbfc2
r368: bugfix - wrong CIGAR when bridging 3 contigs
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In this case, bwa_fix_xref() will return insane coordinates. The old version
did not check the return status and write wrong CIGAR. This bug only happen to
very short assembly contigs.
2013-03-18 20:49:32 -04:00
c862a1a396
Merge branch 'master' into master_fixes
2013-03-18 13:35:12 +00:00
9346acde1b
Release bwa-0.7.3a-r367
...
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
dd51177837
r365: bugfix - wrong alignment (right mapping)
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The bug only happens when there is a 1bp del and 1bp ins which are close to the
end and there are no other substitutions or indels. In this case, bwa mem gave
a wrong band width.
2013-03-15 11:59:05 -04:00
e5355fe3a0
r364: bug in mem pairing (no effect with -A=1)
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Forgot to adjust for matching score. This bug has no effect when -A takes the
default value.
2013-03-14 22:01:26 -04:00
cca27c1ef5
Merge branch 'master' into master_fixes
...
Conflicts:
bwamem.c
bwamem_pair.c
example.c
2013-03-13 12:12:28 +00:00
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
c29b176cb6
r362: bugfix - occasionally wrong TLEN
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Use the 0.7.2 way to compute TLEN
2013-03-12 00:14:36 -04:00
aa7cdf4bb3
r361: flag proper pair even if multi-primary
...
Up to here, all the features in my checklist have been implemented.
2013-03-12 00:00:04 -04:00
dab5b17c1a
r360: output alternative primary alignments in XA
2013-03-11 23:43:58 -04:00
6c665189ad
r359: identical output to 0.7.2 (without -a)
2013-03-11 23:16:18 -04:00
9228e48efd
Merge branch 'master' into master_fixes
...
Conflicts:
Makefile
2013-03-11 13:50:49 +00:00
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.
...
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
66c9783daf
r345: bugfix in mem - wrong mate strand for unmap
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Received a clean bill from Picard
2013-03-08 13:15:43 -05:00
274c0ac96c
r343: bugfix in mem - wrong mate info for unmap
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SAM generation is always among the nastiest bits. I would need to refactor at
some point (hardly happening).
2013-03-08 12:40:31 -05:00
017be45407
r342: bugfix in bwasw - AS is off by one
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but I do not understand why the old code does not have the same problem.
2013-03-08 12:06:45 -05:00
aabd990e8f
Merge branch 'master' into master_fixes
...
Conflicts:
Makefile
bwape.c
bwase.c
bwtsw2_aux.c
stdaln.c
2013-03-08 16:46:45 +00:00
b5b50ac8da
r341: bugfix - wrong mate position
...
when one end is mapped with a score less than -T. Caused by the -T option.
2013-03-07 21:35:57 -05:00
b0a76884e8
r340: feature freeze; updated the manpage
...
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
503ca9ed2e
r339: pemerge - expose some settings to CLI
2013-03-07 11:22:19 -05:00
1cadfa1552
r338: pemerge - fixed memory leaks; multithreading
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pemerge is actually quite slow.
2013-03-07 11:14:52 -05:00
3e3236dfc4
r337: mem - always read even number of reads
...
In the old code, we may read odd number of reads from an interleaved fastq.
2013-03-07 11:00:15 -05:00
72817b664e
r336: fine tuning pemerge
2013-03-06 23:38:07 -05:00
557d50c7e1
r335: fixed a compiling error
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Caused by the last change
2013-03-06 21:57:13 -05:00
042e1f4442
r334: added pemerge to bwa
2013-03-06 21:55:02 -05:00
5fbd454682
r332: added output threshold
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Otherwise there are far too many short hits
2013-03-05 22:49:38 -05:00
6476343a83
r331: rewrote CIGAR generation for bwa-short
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When backtracking, bwa-short does not keep the detailed alignment or the exact
start and end positions. To find the boundary and the CIGAR, the old code does
a global alignment with a small end-gap penalty. It then deals with a lot of
special cases to derive the right position and CIGAR, which are actually not
always right. It is a mess.
As the new ksw.{c,h} does not support a different end-gap penalty, the old
strategy does not work. But we get something better. The new code finds the
boundaries with ksw_extend(). It is cleaner and gives more accurate CIGAR in
most cases.
2013-03-05 19:56:37 -05:00
98f8966750
r329: ditch stdaln.{c,h}; no changes to bwa-mem
...
stdaln.{c,h} was written ten years ago. Its local and SW extension code are
actually buggy (though that rarely happens and usually does not affect the
results too much). ksw.{c,h} is more concise, potentially faster, less buggy,
and richer in features.
2013-03-05 12:00:24 -05:00
8a078cc16d
Merge branch 'master' into master_fixes
...
Conflicts:
bntseq.c
bwamem.c
2013-03-05 10:21:07 +00:00
Rob Davies
Heng Li