depristo
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6ffcaa0afe
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Can run R scripts on the command line
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3750 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-09 00:13:18 +00:00 |
rpoplin
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7f97041875
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Update to AnalyzeCovariates to make the histogram of PairedReadOrder look a little nicer
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2575 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-13 20:26:31 +00:00 |
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rpoplin
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562db45fa5
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Sites that were marked NO_DINUC no longer get dinuc-corrected but are still recalibrated using the other available covariates. Solid cycle is now the same as Illumina cycle pending an analysis that looks at the effect of PrimerRoundCovariate. Solid color space methods cleaned up to reduce number of calls to read.getAttribute(). Polished NHashMap sort method in preparation for move to core/utils. Added additional plots in AnalyzeCovariates to look at reported quality as a function of the covariate.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2451 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-28 20:19:37 +00:00 |
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rpoplin
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12ec154f01
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Make the AnalyzeCovariate plots look a little nicer when there are a small number of data points
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2298 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-09 21:22:40 +00:00 |
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rpoplin
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855face681
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Histogram of covariate values now goes from 0 to max value which makes it look nicer in most cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2259 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-04 14:44:03 +00:00 |
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rpoplin
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985daec76e
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Fixed problem with integer overflow in R scripts.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2258 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-04 14:24:49 +00:00 |
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rpoplin
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2508deca37
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Prevented data points with fewer than N observations from going off the edge of the plots
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2257 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-04 13:55:43 +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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9c597309d3
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Changed the sizes of the dots and bars on the plots generated by the R script which is called from AnalyzeCovariates.java
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2223 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-02 19:47:48 +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 |