kiran
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5b8502745a
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Added an epsilon (1e-4) to the tertiary and quaternary base hypotheses.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@488 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-22 00:01:37 +00:00 |
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kiran
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2ac240d78b
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Removed an extraneous print statement.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@487 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 23:36:36 +00:00 |
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kiran
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0149c887ff
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Fixed a bug wherein the residual probability was not being distributed properly when a file had secondary probs and the best and next-best base agreed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@486 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 23:36:09 +00:00 |
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kiran
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dac76f041b
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Added some methods to retreive the probability distributions of individual bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@484 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 22:26:25 +00:00 |
depristo
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72a3d84ed2
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General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@418 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 22:13:10 +00:00 |