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494 Commits (114901b005fa505fa87a5ee99a0b6d0e1bccaecb)

Author SHA1 Message Date
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
Rob Davies 925aa6f60d Added Makefile.bak and bwamem-lite to .gitignore 2013-03-13 09:18:18 +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
Heng Li 0f88103d2a SAM almost identical to 0.7.2 2013-03-11 23:01:51 -04:00
Heng Li 26f4c704ed drop the old SAM writer 2013-03-11 22:24:54 -04:00
Heng Li 0b0455ca51 replace PE; BUGGY right now!! 2013-03-11 22:18:23 -04:00
Heng Li ebb45dc42e new code works for SE 2013-03-11 21:59:15 -04:00
Heng Li c7edaa8e84 to test the new sam writer... 2013-03-11 21:55:52 -04:00
Heng Li 47952b6f3f drop an unnecessary member from mem_aln_t 2013-03-11 21:35:32 -04:00
Heng Li 8f0d439913 prepare to replace the SAM printing code 
This move is dangerous as SAM printing is very complex, but it will benefit in
the long run. The planned change will reduce the redundancy, improves clarity
and most importantly makes it much easier to output multiple primary hits in an
optional tag.
 2013-03-11 21:25:17 -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 740d2c1314 Match to 'N' costs -1, instead of 0. 
This is to prevent alignment through 'N'.
 2013-03-09 18:03:57 -05:00
Heng Li 9ea7f83974 Emergent bugfix: wrong TLEN sign 
It is interesting that Picard did not find the issue.
 2013-03-09 18:03:15 -05:00
Heng Li 1d132a546d Release 0.7.1-r347 2013-03-08 15:30:06 -05:00
Heng Li 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
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 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
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
Rob Davies aabd990e8f Merge branch 'master' into master_fixes 
Conflicts:
	Makefile
	bwape.c
	bwase.c
	bwtsw2_aux.c
	stdaln.c
 2013-03-08 16:46:45 +00:00
Heng Li 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
Heng Li 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
Heng Li 503ca9ed2e r339: pemerge - expose some settings to CLI 2013-03-07 11:22:19 -05:00
Heng Li 1cadfa1552 r338: pemerge - fixed memory leaks; multithreading 
pemerge is actually quite slow.
 2013-03-07 11:14:52 -05:00
Heng Li 3e3236dfc4 r337: mem - always read even number of reads 
In the old code, we may read odd number of reads from an interleaved fastq.
 2013-03-07 11:00:15 -05:00
Heng Li 72817b664e r336: fine tuning pemerge 2013-03-06 23:38:07 -05:00
Heng Li 557d50c7e1 r335: fixed a compiling error 
Caused by the last change
 2013-03-06 21:57:13 -05:00
Heng Li 042e1f4442 r334: added pemerge to bwa 2013-03-06 21:55:02 -05:00
Heng Li 773b86331b De-overlap paired-end reads 2013-03-06 19:23:45 -05:00
Heng Li 5fbd454682 r332: added output threshold 
Otherwise there are far too many short hits
 2013-03-05 22:49:38 -05:00
Heng Li 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