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
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
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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
a76b75f41e
Merge pull request #14 from drkeoni/master
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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
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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
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
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
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
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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
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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
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
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
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
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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
64d92d26df
more documentation in ksw.h
2013-02-27 21:40:46 -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
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
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
ee80fb8bd0
Test each seed to see if extension is needed
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The old version wastefully extends many seeds contained in an aligned region
found before. While this wastes little time for short reads, it becomes a
serious defect for long query sequences.
This is an attempt to fix this problem, but more tuning are needed.
2013-02-26 22:55:44 -05:00
acd1ab607b
r297: reduce wasteful SW extension
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This is particularly important for long sequences
2013-02-26 16:26:46 -05:00
Rob Davies
Heng Li
Jon Sorenson