depristo 9fe71dc452 Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4562 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-22 20:35:53 +00:00
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R	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.	2009-12-02 16:47:35 +00:00
java/src/org/broadinstitute/sting	Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct.	2010-10-22 20:35:53 +00:00
python	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.	2009-12-02 16:47:35 +00:00