740d2c1314
Match to 'N' costs -1, instead of 0.
...
This is to prevent alignment through 'N'.
2013-03-09 18:03:57 -05:00
9ea7f83974
Emergent bugfix: wrong TLEN sign
...
It is interesting that Picard did not find the issue.
2013-03-09 18:03:15 -05:00
1d132a546d
Release 0.7.1-r347
2013-03-08 15:30:06 -05:00
5370bb23a3
Updated NEWS; added stddef.h for size_t
...
I thought size_t is defined in stdlib.h, but it is not always.
2013-03-08 14:14:42 -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
af7b4d8980
gcc wrongly thinks a variable may be uninitialized
...
It should always be initialized. To avoid a warning, made a change.
2013-03-08 12:45:50 -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
...
but I do not understand why the old code does not have the same problem.
2013-03-08 12:06:45 -05:00
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
...
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
773b86331b
De-overlap paired-end reads
2013-03-06 19:23:45 -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
...
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
a76b75f41e
Merge pull request #14 from drkeoni/master
...
Small fix for possible compile problem on Ubuntu systems
2013-03-05 12:57:10 -08:00
25366c7220
Fixing problem with linking to libm on some Ubuntu systems (I see this on machine running 11.04, kernel 3.0.0-14-virtual). Changing order of -lm on the command line seems to do the trick and should be tolerated in other environments.
2013-03-05 20:48:16 +00:00
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
bb37e14d02
replace aln_global in bwase.c
2013-03-05 10:38:47 -05:00
e6c262594f
bwa-sw: ditch stdaln
2013-03-05 10:12:38 -05:00
086c9d0e7d
bwa-sw: use bwa_gen_cigar() for cigar generation
2013-03-05 09:54:49 -05:00
07921659cf
move mem_fill_scmat() to bwa.{h,c}
2013-03-05 09:38:12 -05:00
efd9769b07
r324: a little code cleanup
...
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
d6096c3f99
bugfix: caused by the latest change
2013-03-04 18:41:57 -05:00
59bc9341f6
code backup; more changes coming later
2013-03-04 17:29:07 -05:00
733410b50d
r320: speed up very long sequence alignment
...
100-200bp read alignment should not be affected at all.
2013-03-04 14:43:49 -05:00
40f1214736
change to debugging code only
2013-03-04 11:52:11 -05:00
7e00dbcac5
r317: bugfix - out-of-range extension
...
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
1a451df800
prepare to ditch stdaln.{h,c}
2013-03-04 10:32:33 -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
c5434ac865
r313: release bwa-0.7.0
2013-02-28 15:56:05 -05:00
39fcde9c19
updated NEWS further
2013-02-28 00:58:24 -05:00
f3cff1c609
r311: even tighter bw for CIGAR
2013-02-27 23:59:50 -05:00
a33b9c0633
tighter bw for cigar SW
2013-02-27 23:40:46 -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
...
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
64d92d26df
more documentation in ksw.h
2013-02-27 21:40:46 -05:00
4bb0bdddca
r306: introduce clipping penalty
...
More clipping leads to more severe reference bias. We should not clip the
alignment unless necessary.
2013-02-27 21:13:39 -05:00
b7791105bc
r305: in NEWS, convert TAB to space
2013-02-27 16:56:54 -05:00
aef179a580
r304: prepare release notes (not released yet)
2013-02-27 16:55:07 -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
Heng Li
Jon Sorenson