depristo
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89f3ee614a
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minor printing fix
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2492 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-30 22:14:50 +00:00 |
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depristo
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fcc80e8632
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Completely rewritten duplicate traversal, more free of bugs, with integration tests for count duplicates walker validated on a TCGA hybrid capture lane.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2458 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-28 23:56:49 +00:00 |
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depristo
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0d2a761460
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Bugfix for minBaseQuality to ignore deletion reads. LocusMismatch walker now allows us to skip every nths eligable site
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2357 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-15 14:38:39 +00:00 |
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depristo
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56467df49a
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minor improvements to snpSelector to work with hapmap chip VCF files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2343 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-13 17:59:32 +00:00 |
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depristo
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b2dfe85648
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Better support for reading truth file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2307 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-10 12:16:05 +00:00 |
chartl
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6a4118ad3c
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grr, ought to actually assign it to the TRUTH_CALLS variable
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2302 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-09 23:31:46 +00:00 |
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chartl
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987fced151
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Should read truth data from the parser options rather than direct from args
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2301 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-09 23:26:26 +00:00 |
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depristo
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2632cb6b58
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minor improvements to snp selector
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2275 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-07 03:37:14 +00:00 |
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depristo
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2c7cb912f0
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Bug fixes for mixed none/valued attributes. also now assigns fake float values for display, if requested, for covariates using the -plottable flag
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2253 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-03 23:52:35 +00:00 |
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depristo
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dbb8b86ed1
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Minor updates to correctly handle emitting FN calls
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2231 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-02 22:53:17 +00:00 |
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depristo
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8a87d5add1
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misc. bug fixes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2212 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-02 14:36:03 +00:00 |
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depristo
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c93d37d9fb
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continuing improvements in output of snpSelector
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2198 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-01 15:42:06 +00:00 |
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depristo
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2ea93385be
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Better support for comparison to truth. Now emits FP rates for each covariate if a truth file is provided. Also now writes out a detailed recal.log file that can be parsed directly into R
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2179 348d0f76-0448-11de-a6fe-93d51630548a
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2009-11-29 22:20:40 +00:00 |
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depristo
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65da04ca85
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Now uses the theoretically correct relationship between SNP FP and TP ratios for Illumina data. maxQ score for a snp is now 60
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2168 348d0f76-0448-11de-a6fe-93d51630548a
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2009-11-25 22:08:12 +00:00 |
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depristo
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03342c1fdd
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Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2154 348d0f76-0448-11de-a6fe-93d51630548a
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2009-11-25 03:51:41 +00:00 |
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depristo
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bc35a34f60
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More informative printing, no longer prints tons of NaN warnings
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2139 348d0f76-0448-11de-a6fe-93d51630548a
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2009-11-24 15:45:48 +00:00 |
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depristo
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da7de9960b
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General bug fixes for snpSelector. More robust error checking and handling of NaN values.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2106 348d0f76-0448-11de-a6fe-93d51630548a
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2009-11-21 14:48:29 +00:00 |
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depristo
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52494d8176
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cleanup of SNP selector -- ready for some additional testing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2042 348d0f76-0448-11de-a6fe-93d51630548a
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2009-11-13 21:46:31 +00:00 |
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depristo
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1a4d071d37
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Better snpSelector, plus VCFmerge tool
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2022 348d0f76-0448-11de-a6fe-93d51630548a
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2009-11-11 22:02:57 +00:00 |
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depristo
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3990c6d950
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snpSelector v3 -- bootstrapping support and VCF output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2004 348d0f76-0448-11de-a6fe-93d51630548a
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2009-11-09 22:48:51 +00:00 |
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depristo
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f777c806d6
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snpSelector v2 -- code refactoring and support for comparison with known truth. Looks great.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1986 348d0f76-0448-11de-a6fe-93d51630548a
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2009-11-07 19:32:12 +00:00 |
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depristo
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7cb51dbc31
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snpSelector v1 -- and supporting changes to VCF reader
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1983 348d0f76-0448-11de-a6fe-93d51630548a
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2009-11-06 23:00:46 +00:00 |