kiran
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b0cc763eb5
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Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does *not* affect the default functionality of the standard PileupWalker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@969 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-10 17:31:00 +00:00 |
depristo
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13be846c2a
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qualsAsInt argument for Pileup -- fixing stupid bug [again]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@898 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-04 18:52:12 +00:00 |
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depristo
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97c8ff75dd
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qualsAsInt argument for Pileup -- fixing stupid bug
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@897 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-04 18:51:17 +00:00 |
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depristo
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9de3e58aa8
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qualsAsInt argument for Pileup
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@896 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-04 18:37:39 +00:00 |
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depristo
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dc17a5661d
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Better accessors for dealing with second base prob pileups
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@785 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 22:25:16 +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 |
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depristo
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24722a442e
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Slight code cleanup
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 22:21:36 +00:00 |
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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 |