rpoplin
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71ecbe75d7
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AnalyzeCovariates would crash with 'too many open files' exception when spawning Rscript jobs for every read group at once. It now waits for some to finish before spawning the rest.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2508 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-06 14:19:02 +00:00 |
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rpoplin
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0a6bd5a270
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CycleCovariate is now one-based so that 0 and -0 don't collide with each other. Solid recal modes now only change the inconsistent base and the previous base (along the direction of the read) instead of both the bases before and after. Removed estimatedNumberOfBins from the Covariate interface because it wasn't being used.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2498 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-04 20:52:15 +00:00 |
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rpoplin
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80658fd99e
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AnalyzeCovariates gets the same performance improvements as the recalibrator. NHashMap class is removed completely.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2483 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-30 18:10:10 +00:00 |
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rpoplin
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96c4929b3c
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Recalibrator now uses NestedHashMap instead of NHashMap. The keys are now nested hash maps instead of Lists of Comparables. These results in a big speed up (thanks Tim!). There is still a little bit of clean up to do, but everything works now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2474 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-29 21:01:32 +00:00 |
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rpoplin
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fcc52fbcd1
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Fixed the build. Added missing import line.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2454 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-28 21:26:00 +00:00 |
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rpoplin
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4fa4e95fbc
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Updated AnalyzeCovariates to extend org.broadinstitute.sting.utils.cmdLine.CommandLineProgram and use the standard argument parsing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2335 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-11 21:57:18 +00:00 |
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rpoplin
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46f3d3e39b
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Added comments to AnalyzeCovariates and R scripts. R script prevents residuals from going off the edge of the plot. Added skeleton code to the recalibration walkers showing how we plan to handle SOLID reference inserting behavior.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2233 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-02 23:15:52 +00:00 |
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rpoplin
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67179e2412
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Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2215 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-02 16:47:35 +00:00 |