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
...
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
...
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
...
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
...
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
...
This is particularly important for long sequences
2013-02-26 16:26:46 -05:00
54ab3bbec7
Dropped solid2fastq.pl
...
SOLiD is not supported any more.
2013-02-26 14:35:03 -05:00
98787f0ae0
r295: generate NM
2013-02-26 13:36:01 -05:00
32f2d60a2e
r294: bugfix - -M not working
2013-02-26 13:14:33 -05:00
619ac4f93d
r293: bugfix - wrong RG type in SAM output
2013-02-26 13:03:35 -05:00
c6b226d719
r292: fixed a very stupid bug on CLI
...
I was thinking 0x10 or 16, but wrote 0x16...
2013-02-26 12:49:48 -05:00
bfb2583d7f
r291: summary - bwt.c micro optimization
2013-02-26 12:10:19 -05:00
aa92c720b5
cleanup bwt_occ()
2013-02-26 12:09:28 -05:00
80e1137a6c
move bwt_invPsi() from bwt.h to bwt.c
2013-02-26 11:57:36 -05:00
fd67064207
removed an unnecessary condition
2013-02-26 11:51:03 -05:00
264d5e42e5
simplified bwt_occ4() a little
2013-02-26 11:49:39 -05:00
c848b44481
code backup
2013-02-26 11:22:24 -05:00
174fe0f1d5
code backup: less dependent on gcc optimization
2013-02-26 11:14:19 -05:00
e70c7c2a71
r284: amend cross-reference hit
...
I really hate this: complex and twisted logic for a nasty scenario that almost
never happens to short reads - but it may become serious when the reference
genome consists of many contigs.
On toy examples, the code seems to work. Don't know if it really works...
2013-02-26 00:03:49 -05:00
61dd3bf13a
r283: prepare for fixing cross-ref aln
2013-02-25 22:49:15 -05:00
77b5b586ad
r282: set min split_len to read length
2013-02-25 17:29:35 -05:00
Heng Li
Jon Sorenson