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 |
kiran
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83e1454a11
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Added a method to determine the fraction of a sequence that's taken up by the most frequent base.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@781 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 20:35:31 +00:00 |
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kiran
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1a9d5cea29
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Added a method to reverse-complement a String object, preserving 'N' and '.' bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@776 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 19:39:39 +00:00 |
andrewk
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0219d33e10
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QualityUtils: added reverse function to reverse an array of bytes (and not complement it), BaseUtils: split qualToProb into itself and qualToErrProb, CovariateCounterWalker and LogisticRecalibrationWalker: several changes including a properly acocunting (only partly complete) for reversing AND complementing bases that are negative strand, PrintReadsWalker: created option to output reads to a BAM file rather than just to the sceern (useful for creating a downsampled BAM file)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@770 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 18:30:45 +00:00 |
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kiran
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68c9455c0f
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Moved the base complement method to BaseUtils.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@711 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 18:57:48 +00:00 |
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kiran
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ca66cccd2f
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Privatized constructor to prevent instantiation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@506 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-23 17:45:39 +00:00 |
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kiran
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5b2a7c9c23
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Added some methods to complement a single simple base ([AaCcGgTt]) and reverse-complement a byte-array of bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@483 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 22:25:33 +00:00 |
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kiran
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40ea22eb17
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Added some methods to return the cross-talk partner base of a given base or base index.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@400 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 14:49:12 +00:00 |
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kiran
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5e96ab6161
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Helpful functions for converting a base (char) to a base index (A:0, C:1, G:2, T:3, alphabetical and consistent with Illumina conventions to minimize confusion.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@373 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-13 00:46:23 +00:00 |