rpoplin 210c4c9913 AnalyzeAnnotations now makes plots for the value in the QUAL column as if it were an annotation. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2771 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-03 20:33:15 +00:00
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alignment	Misc bug fixes.	2010-01-05 14:48:19 +00:00
analyzecovariates	Added an option to AnalyzeCovariates to set the max value of the histograms to make them easier to directly compare.	2010-01-31 23:13:57 +00:00
gatk	Add an alternate implementation of the BAM file reader that keeps the entire index in memory. Initial revision of BAMFileStat, a tool to inspect BAM file BGZF blocks and index entries.	2010-02-03 19:48:15 +00:00
oneoffprojects	improvements to variant eval 2. Now has titv calculations and mendelian violation detect support. we only make ~80 mendelian violations in 380K calls for the YRI trio, in case you are interested	2010-02-03 16:03:19 +00:00
playground	AnalyzeAnnotations now makes plots for the value in the QUAL column as if it were an annotation.	2010-02-03 20:33:15 +00:00
utils	Bunch of oneoff stuff that I don't want to lose. Also:	2010-02-01 21:35:10 +00:00