depristo
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5289230eb8
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Version 0.2.1 (released) of the TableRecalibrator
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 22:50:55 +00:00 |
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depristo
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0a50f2e160
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Updated and near final version of tabular recalibration system. Uses 'yates' correction for low-occupancy quality bins. Faster and more robust handling of input and output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1082 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-24 03:52:12 +00:00 |
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depristo
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d748c85dc4
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Cleaned code and reorganized -- moving in the right direction for v2
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1052 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-18 22:28:34 +00:00 |
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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 |
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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 |
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 |
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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64c65c7751
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New methods to generated compressed SQ quality elements in line with the SAM spec.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@699 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 16:50:31 +00:00 |
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depristo
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71e8f47a6c
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boundQual function for capping qual values
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@623 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-07 18:04:18 +00:00 |
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depristo
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1cc5e74435
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More ways to access quality utils
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@573 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-30 22:12:07 +00:00 |
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kiran
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59b2e6a90f
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Added some stuff for retreiving the base index and probability of a compressed base.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@329 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-08 15:52:58 +00:00 |
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kiran
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ef06924f73
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JavaDocs!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@290 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-03 19:19:17 +00:00 |
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kiran
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b854c24575
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Oops. I gave this method the wrong name first time around.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@283 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-03 15:46:26 +00:00 |
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kiran
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a8a6c63a32
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A class with some static methods that aid the manipulation of quality scores and probabilities (including a method to compress a base and quality score into a byte for SAM output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@271 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-02 22:06:15 +00:00 |