331d6db783
Reduce file handle usage.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2503 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-05 18:03:01 +00:00
38a030f2ba
Finishing off data transfer conduits for single alignment generator.
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Misc bug fixes elsewhere.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2101 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 15:21:59 +00:00
a95302fe98
Single alignment generator, another checkpoint. Does generate single alignments, but some of the data still
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needs to plumbed through and it may leak memory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2095 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 21:20:03 +00:00
a972b2769f
Checkpoint. Add first phase of single alignment interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2094 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 19:03:43 +00:00
f5818c0cda
Fix max edit distance to ensure interface similarity between our aligner and
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'bwa aln'.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2043 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 22:18:56 +00:00
0c2a957ae0
Better configuration support. Now supports everything that people have expressed interest in except edit distance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2021 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 20:54:49 +00:00
43c3ee61d5
Fix minor mapping quality bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1973 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-04 14:33:23 +00:00
c63af32fc7
The BWA/C bindings were triggering the local aligner to repeatedly reload the
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ref genome. Make sure the reference genome is cached.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1961 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 00:01:55 +00:00
1896f334d9
Fixed collection of bugs in reads aligning to multiple locations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1955 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 04:02:09 +00:00
1f0d852a48
Fix bug where alignments with indels would be busted because bwa reverses
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the read bases to undo a previous read base reverse that doesn't occur in the
libbwa codepath.
Also fixed some memory management issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1938 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 21:33:13 +00:00
f04b80d7db
Fixed epic memory leak.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1934 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 16:32:43 +00:00
c9a3707cfd
Initial version of BWA/C bindings. Still lots of squirrels roaming the code.
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- Some cigar strings aren't right.
- Memory leaks.
- BWA codebase changes aren't committed to BWA tree.
- Aligner interface butchered to support BWA/C-style alignments.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1928 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 21:37:49 +00:00
hanna