gatk-3.8

Author	SHA1	Message	Date
rpoplin	67179e2412	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	2009-12-02 16:47:35 +00:00
ebanks	05923f7fba	Started transition to oneoffprojects. Moved/killed a few other walkers (with permission). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2204 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-01 21:19:02 +00:00
ebanks	084337087e	Removing deprecated code and walkers for which I had the green light from repository. Moved piecemealannotator and secondarybases to archive. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2195 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-01 05:58:20 +00:00
ebanks	2c16c18a04	Move Andrey's old indel code (plus MSG accuracy test, which depends on it) to archive. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2194 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-01 05:29:00 +00:00