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145 Commits (599e8407799ec603c3d36e9275cea959ede3a0bf)

Author SHA1 Message Date
Heng Li 599e840779 r397: multi changes/bugfixes to bwa-backtrack 
1. Check .sai versioning
2. Keep track of #ins and #del during backtrack
3. Use info above to get accurate aligned regions; don't call SW extension any more
4. Identify alignment crossing the for-rev boundary
5. Fixed a bug in printing the XA tag: ungapped alignments missing
 2013-05-24 16:28:18 -04:00
Heng Li bde5005f39 r396: er... the new tag is named SA not SP 2013-05-23 12:48:18 -04:00
Heng Li 3d2450ed97 r395: bugfix - hard clipping not applied on revaln 2013-05-23 12:45:14 -04:00
Heng Li 9441bb7f2a r394: added future plan 2013-05-22 20:02:53 -04:00
Heng Li 9a6abe51b6 r391: better method to resolve xref alignment 
The old method does not work when the alignment bridges three chr. This may
actually happen often. The new method does not work all the time, either, but
should be better than the old one. It is also simpler, arguably.
 2013-05-22 18:57:51 -04:00
Rob Davies e88529687f Merge branch 'master' into master_fixes. Merged up to r389. 
Conflicts:
	bwamem.c
	kopen.c
 2013-04-29 12:09:30 +01:00
Heng Li 1a2bd2cf91 r389: return non-zero upon errors 2013-04-27 10:08:01 -04:00
Heng Li 19cb7cd7ed r388: cleanup mem_process_seqs() interface 
Print output outside the function and allow to feed insert size distribution.
 2013-04-26 12:31:18 -04:00
Heng Li 8896cb942e r386: bugfix - samse/pe segfault 
This happens when a read is aligned across the forward-reverse boundary.
 2013-04-24 16:00:02 -04:00
Rob Davies b3d0a13b32 Merge branch 'master' into master_fixes. Merged up to release bwa-0.7.4-r385. 2013-04-23 17:31:34 +01:00
Heng Li c14aaad1ce Released bwa-0.7.4-r385 2013-04-23 11:40:56 -04:00
Heng Li 2f6897c72b r384: don't compile bwamem-lite by default 2013-04-23 11:27:30 -04:00
Heng Li 78ed00021f r384: updated NEWS 2013-04-23 11:25:46 -04:00
Rob Davies 4cb5110d03 Merge branch 'master' into master_fixes 2013-04-22 09:51:07 +01:00
Heng Li f6ae0d4d0f r382: similar treatment in bwa-sw (see r381) 2013-04-19 17:52:06 -04:00
Heng Li 3f8caef33c r381: fixed a bug when upper bound < max read len 2013-04-19 17:44:35 -04:00
Heng Li db7a98636f r380: er... another compiling error 2013-04-19 12:04:44 -04:00
Heng Li f0c94d80d1 r379: fixed compiling error 2013-04-19 12:04:00 -04:00
Heng Li be11e27e12 r378: bugfix - wrong CIGAR 
This is actually caused by a bug in SSE2-SW, where the query begin may be
smaller than the true one if there is an exact tandem repeat.
 2013-04-19 12:00:37 -04:00
Heng Li 2087dc162f r377: increased unpaired penalty from 9 to 17 
This leads to more aggressive pairing - more properly paired reads. I have
found a few cases where, for example, read1 is umambiguously mapped to chr20
while its 100bp mate has a perfect match to another chr but has 3 mismatches
and 1 deletion when it is paired with read1 on chr20. With longer reads, it
seems that the chr20 hit is correct, although it is not obvious how this
happened in evolution.
 2013-04-17 16:50:20 -04:00
Rob Davies 3dd10bd7db Merge branch 'master' into master_fixes 2013-04-12 16:20:13 +01:00
Rob Davies 90ecd344ba Merge branch 'master' into master_fixes. Merged up to master r375. 
Conflicts:
	bwt.c
 2013-04-11 11:15:39 +01:00
Heng Li 499cf4c00d r376: reduce wasteful seed extension 
mainly for contig alignment
 2013-04-10 12:18:56 -04:00
Heng Li 47520134e7 r375: fixed compiling errors by the last change 2013-04-10 11:04:32 -04:00
Heng Li 3d8a8c1e37 r374: fix - clipping penalty not always working 
This only happens to gaps where mem underestimates the bandwidth without
considering the clipping penalty.
 2013-04-10 01:09:37 -04:00
Heng Li 53bb846407 r373: optionally distable mate rescue 2013-04-09 16:13:55 -04:00
Heng Li d64eaa851d fixed an issue caused by a Mac/Darwin bug 
On Mac/Darwin, it is not possible to read >2GB data with one fread().
 2013-04-09 15:17:04 -04:00
Heng Li d7ca0885eb r371: extend overlapping seeds 
to avoid misalignment in tandem repeats
 2013-04-04 00:43:43 -04:00
Heng Li 1e118e0823 r370: suppress "D" at the end of a cigar 
This is caused by seeds in tandem repeats, in which case, bwa-mem may not
extend the true seed. The change in this commit is only a temporary cure.
 2013-04-03 23:57:19 -04:00
Rob Davies c89756e2b0 Merge branch 'master' into master_fixes 2013-03-19 12:11:51 +00:00
Heng Li 8437cd4edd r369: bugfix - segfault caused by the last change 
Sigh... Even the simplest change can lead to new bugs.
 2013-03-19 01:04:57 -04:00
Heng Li 1e3cadbfc2 r368: bugfix - wrong CIGAR when bridging 3 contigs 
In this case, bwa_fix_xref() will return insane coordinates. The old version
did not check the return status and write wrong CIGAR. This bug only happen to
very short assembly contigs.
 2013-03-18 20:49:32 -04:00
Rob Davies c862a1a396 Merge branch 'master' into master_fixes 2013-03-18 13:35:12 +00:00
Heng Li 9346acde1b Release bwa-0.7.3a-r367 
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
Heng Li 7dec00c217 Release BWA-0.7.3-r366 2013-03-15 12:51:53 -04:00
Heng Li dd51177837 r365: bugfix - wrong alignment (right mapping) 
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
Heng Li e5355fe3a0 r364: bug in mem pairing (no effect with -A=1) 
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
Rob Davies cca27c1ef5 Merge branch 'master' into master_fixes 
Conflicts:
	bwamem.c
	bwamem_pair.c
	example.c
 2013-03-13 12:12:28 +00:00
Heng Li bdf34f6ce7 r363: XA=>XP; output mapQ in XP 
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
Heng Li c29b176cb6 r362: bugfix - occasionally wrong TLEN 
Use the 0.7.2 way to compute TLEN
 2013-03-12 00:14:36 -04:00
Heng Li aa7cdf4bb3 r361: flag proper pair even if multi-primary 
Up to here, all the features in my checklist have been implemented.
 2013-03-12 00:00:04 -04:00
Heng Li dab5b17c1a r360: output alternative primary alignments in XA 2013-03-11 23:43:58 -04:00
Heng Li 6c665189ad r359: identical output to 0.7.2 (without -a) 2013-03-11 23:16:18 -04:00
Rob Davies 9228e48efd Merge branch 'master' into master_fixes 
Conflicts:
	Makefile
 2013-03-11 13:50:49 +00:00
Heng Li 5581cb9152 Release bwa-0.7.2-r351 
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
Heng Li 2d01a297fb Improving 'properly paired' flag. 
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
Heng Li 1d132a546d Release 0.7.1-r347 2013-03-08 15:30:06 -05:00
Heng Li 66c9783daf r345: bugfix in mem - wrong mate strand for unmap 
Received a clean bill from Picard
 2013-03-08 13:15:43 -05:00
Heng Li 274c0ac96c r343: bugfix in mem - wrong mate info for unmap 
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
Heng Li 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