ebanks f742980864 1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon. ... 2. Moved Jared's VCFTool code into archive so that everything would compile. 3. Added the vcf reference base (needed for indels) as an attribute to the VariantContext from the reader. 4. TribbleRMDTrackBuilderUnitTest was complaining that a validation file didn'r exist, so I commented it out. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3835 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-20 06:16:45 +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	1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon.	2010-07-20 06:16:45 +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