c862a1a396
Merge branch 'master' into master_fixes
2013-03-18 13:35:12 +00:00
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
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
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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
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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
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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.
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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
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
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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
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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
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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
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
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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
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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
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Conflicts:
bntseq.c
bwamem.c
2013-03-05 10:21:07 +00:00
efd9769b07
r324: a little code cleanup
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The changes after r317 aim to improve the performance and accuracy for very
long query alignment. The short-read alignment should not be affected. The
changes include:
1) Z-dropoff. This is a variant of blast's X-dropoff. I orginally thought this
heuristic only improves speed, but now I realize it also reduces poor
alignment with long good flanking alignments. The difference from blast's
X-dropoff is that Z-dropoff allows big gaps, but X-dropoff does not.
2) Band width doubling. When band width is too small, we will get a poor
alignment in the middle. Sometimes such alignments cannot be fully excluded
with Z-dropoff. Band width doubling is an alternative heuristic. It is based
on the observation that the existing of close-to-boundary high score
possibly implies inadequate band width. When we see such a signal, we double
the band width.
2013-03-05 00:57:16 -05:00
e0991d6a45
r323: added Z-dropoff, a variant of blast's X-drop
2013-03-05 00:34:33 -05:00
733410b50d
r320: speed up very long sequence alignment
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100-200bp read alignment should not be affected at all.
2013-03-04 14:43:49 -05:00
7e00dbcac5
r317: bugfix - out-of-range extension
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This happens when target region crosses the forward-reverse boundary. This will
almost never happen to short-read alignment.
2013-03-04 11:35:23 -05:00
d35f33b513
r316: don't allocate zero-length memory
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It is not a bug, but Electric Fence does not like that.
2013-03-04 10:22:18 -05:00
35fb7f9fdf
r315: move kopen.o out of libbwa.a
2013-03-01 11:47:51 -05:00
3e4a178e08
r314: cleanup bwamem API
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Don't modify input sequences; more documentations
2013-03-01 11:14:51 -05:00
6beab5f765
Merge branch 'master' into master_fixes
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Merge changes to commit c5434ac
2013-03-01 10:22:49 +00:00
3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
c5434ac865
r313: release bwa-0.7.0
2013-02-28 15:56:05 -05:00
f3cff1c609
r311: even tighter bw for CIGAR
2013-02-27 23:59:50 -05:00
6a4d8c79d8
r309: bugfix - soft clipping missing in example.c
2013-02-27 22:45:18 -05:00
df7c3f0000
r308: added a new API to convert region to CIGAR
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and an example program demonstrating how to do single-end alignment in <50
lines of C code.
2013-02-27 22:28:29 -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
b621d3ae38
r301: left-align indels
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Don't know why the change is working...
2013-02-27 00:42:19 -05:00
65e099df34
r300: fixed an out-of-boundary bug in rare case
2013-02-27 00:37:17 -05:00
0b533385ef
r299: better way to exclude seed
2013-02-27 00:29:11 -05:00
Rob Davies
Heng Li