hanna
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db642fd08b
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Optimization: from 10k reads/sec - 22k reads/sec..
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1819 348d0f76-0448-11de-a6fe-93d51630548a
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2009-10-13 18:07:15 +00:00 |
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hanna
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3b79f9eddc
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Support 'N's and other mismatch characters in the reference.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1721 348d0f76-0448-11de-a6fe-93d51630548a
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2009-09-24 21:41:30 +00:00 |
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hanna
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14477bb48e
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Unidirectional alignments with mismatches now working. Significant refactoring will be required.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1686 348d0f76-0448-11de-a6fe-93d51630548a
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2009-09-22 19:05:10 +00:00 |
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hanna
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c186a49d55
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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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1648 348d0f76-0448-11de-a6fe-93d51630548a
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2009-09-17 23:28:47 +00:00 |