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15 Commits (aece7fa4c78e52cb64cbcd086b8d5b2ee3992a87)

Author SHA1 Message Date
hanna 768f865035 Bulletproofing code. If errors are encountering during the run, turn them 
into JDK exceptions whenever possible instead of random core dumps.  Don't
allow negative values for most of the 'bwa aln' input parameters.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2049 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-14 22:57:16 +00:00
hanna 15c14add4d Repackage the aligner for better partitioning. The C aligner, for example, is now 
partitioned from the Java aligner, and both are partitioned from the more general-
purpose BWT reader.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2045 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 22:55:27 +00:00
hanna f5818c0cda Fix max edit distance to ensure interface similarity between our aligner and 
'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
hanna 0c2a957ae0 Better configuration support. Now supports everything that people have expressed interest in except edit distance. 
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
hanna 637f02f392 BWA/C changes have arrived in svn repository. Remove temporary storage from Sting repository. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2019 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 16:48:21 +00:00
hanna f73dd09399 More preparation for bwa patch: create a crude, minimal build system to build 
against a static library that the bwa compile (now) generates.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1980 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-06 18:41:01 +00:00
hanna 15e80aec3b Temporarily adding changed bwa files to Sting repository until I can pull together the official bwa patch. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1975 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-04 21:46:05 +00:00
hanna 43c3ee61d5 Fix minor mapping quality bug. 
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
hanna c63af32fc7 The BWA/C bindings were triggering the local aligner to repeatedly reload the 
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
hanna 1896f334d9 Fixed collection of bugs in reads aligning to multiple locations. 
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
hanna 2d15891719 Created walkers for alignment, validation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1945 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 15:04:07 +00:00
hanna 1f0d852a48 Fix bug where alignments with indels would be busted because bwa reverses 
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
hanna f04b80d7db Fixed epic memory leak. 
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
hanna c9a3707cfd Initial version of BWA/C bindings. Still lots of squirrels roaming the code. 
- 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 2ee2623926 Move non-java code out of playground. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@154 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 19:31:38 +00:00