56bc4fa21a
Fixed bug where not all alignments were returned if read aligned to multiple locations. Enhanced test suite to validate all alignments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1762 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-04 18:20:20 +00:00
05aa928e3e
Fix off-by-number-of-deletions issue with negative strand reads. Improved performance by factor of 2.5x.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1761 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-03 21:55:18 +00:00
665951f9f0
Support negative strand alignments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1748 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-30 18:10:26 +00:00
d3b1732cca
Start of refactoring effort. Make construction of alignment object simpler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1747 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-30 15:19:31 +00:00
44879c81b0
Add in weights. Massive performance improvements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1722 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 23:19:15 +00:00
3b79f9eddc
Support 'N's and other mismatch characters in the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1721 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 21:41:30 +00:00
08e8d2183a
Indels supported. Variable gap penalties are not yet taken into account.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1720 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 21:03:02 +00:00
b0ec7fc144
More comprehensive testing of BWT (mismatches only) module, and lots of bug fixes.
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Limitations:
1) Can't handle RC alignments.
2) Can't handle indels.
3) Can't handle N's in reference bases.
4) Stops at first hit.
Ran BWT over a test suite of 800k Ecoli reads. After removing alignments with indels / reads with Ns, the remaining reads were aligned with quality 'equal to' that of the alignment stored in the BAM file. In this case 'equal' quality is <= mismatches to the reference as the existing alignment stored in the BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1710 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-23 23:44:59 +00:00
14477bb48e
Unidirectional alignments with mismatches now working. Significant refactoring will be required.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1686 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-22 19:05:10 +00:00
c186a49d55
Time for a reorganization. Repackage generally useful alignment classes lower in the package structure, and create a subpackage for bwa-specific code. Repackage BWA alignment code away from BWT representation. Isolate byte- and word-packing streams in another package that will ultimately be killed off en masse.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1648 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-17 23:28:47 +00:00
hanna