depristo
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7d281296a7
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Finishing checking for building
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1027 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-17 14:12:40 +00:00 |
kiran
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681e67c72c
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Added some methods to generate random bases or random base indexes, optionally disallowing the generation of a specified base or base index.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@943 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-09 00:47:54 +00:00 |
asivache
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3b4dc6e7b5
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added sequencePeriod(String seq, int minPeriod) - finds smallest period equal to or greater than minPeriod for the specified text string seq; this is a trivial (hopefully correct) back-of-the-envelope implementation for a well-known and well-studied problem; there should be more efficient algorithms in the wild
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@925 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-06 23:05:24 +00:00 |
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depristo
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7e7c83ddca
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fixing insidious bugs
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@879 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-02 18:33:45 +00:00 |
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kiran
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454a6d1df7
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Fixed an egregious error in simpleReverseComplement wherein the RC'd string would be composed entirely of the last base.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@804 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-22 19:32:20 +00:00 |
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depristo
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7a979859a9
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Intermediate checking for evaluation -- now supports transition / transversion evaluation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@793 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-22 17:05:06 +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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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 |