depristo
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43fdd31e20
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Significant performance optimization for reduced reads due to better algorithm for including reads in the variable regions. Fixed a critical bug that actually produced multiple copies of the same read in the variable regions with this optimization as well. Scala exploration script updated as well.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6005 348d0f76-0448-11de-a6fe-93d51630548a
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2011-06-16 12:54:59 +00:00 |
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depristo
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44287ea8dc
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ReducedBAM changes to downsample to a fixed coverage over the variable regions. Evaluation script now has filters and eval. commands.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5965 348d0f76-0448-11de-a6fe-93d51630548a
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2011-06-08 19:36:08 +00:00 |
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depristo
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cd293f145b
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More stable reduced reads representation. Bug fixes throughout. No diffs by <1% of sites in an exome, and the majority of these differences are filtered out, or are obvious artifacts. UnitTests for BaseCounts. BaseCounts extended to handle indels, but not yet enabled in the consensus reads.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5939 348d0f76-0448-11de-a6fe-93d51630548a
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2011-06-03 20:11:31 +00:00 |