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
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
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
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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
e70c7c2a71
r284: amend cross-reference hit
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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
30cc8a95d1
fixed an unimportant memory leak
2013-02-25 16:34:19 -05:00
d19e834d84
r280: align two ends in the same thread
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Otherwise odd-number threads may be of different speed from even-number threads.
2013-02-25 15:40:15 -05:00
20aa848b3c
r279: for PE mapq, consider the number of pairs
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If there are a lot of proper pairs, it is more likely that the best pair is
wrong.
2013-02-25 13:00:35 -05:00
9957e04590
r278: don't perform too many mate-sw
2013-02-25 11:56:02 -05:00
e9e5ee6a3d
r277: updated the revision number
2013-02-25 11:34:06 -05:00
0b4a40dc25
updated revision number; to merge into master
2013-02-24 13:34:20 -05:00
545fb87feb
removed another part related to color-space
2013-02-22 17:15:57 -05:00
6ad5a3c086
removed color-space support
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which has been broken since 0.6.x
2013-02-12 10:21:17 -05:00
91debf412b
move smem iterators to bwamem.{c,h}
2013-01-31 13:59:48 -05:00
292f9061ab
r132: optionally copy FASTA/Q comment to SAM
2012-10-26 12:54:32 -04:00
3abfd0743a
r131: r128 plus remote changes
2012-06-28 14:52:18 -04:00
f44edd4fc9
r128: more conservative chaining filter
2012-06-28 14:51:02 -04:00
09ee115dcc
r126: release bwa-0.6.2
2012-06-19 13:29:44 -04:00
29ed2d8287
rename the "api" branch as "master"
2012-06-19 13:13:29 -04:00
d97ff6bf72
r124: updated version number
2012-04-17 20:45:07 -04:00
790df95e1a
updated revision number
2012-04-02 11:43:32 -04:00
bdc953cad9
Tim's suggestion suffix file name with .64
2012-03-29 12:22:51 -04:00
91a4a0c8ea
Release bwa-0.6.1
2011-11-28 09:52:07 -05:00
bf65b6463a
fastmap: optionally output the original query seq
2011-11-24 19:44:21 -05:00
b5170e0efa
output the NM tag
2011-11-24 11:51:38 -05:00
196b50dde3
optionally mark multi-part hits as secondary
2011-11-23 23:39:59 -05:00
Rob Davies
Heng Li
Heng Li