depristo 7c42e6994f FindBugs fixes throughout the code base ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3823 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-18 16:29:59 +00:00
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alignment	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
analyzecovariates	Fix for added EOF in csv file	2010-07-13 16:09:48 +00:00
commandline	Workaround for scala trait erasing parameterized types:	2010-07-07 03:15:10 +00:00
gatk	FindBugs fixes throughout the code base	2010-07-18 16:29:59 +00:00
oneoffprojects	First step in major cleanup/redo of VCF functionality. Specifically, now:	2010-07-16 22:49:16 +00:00
playground	FindBugs fixes throughout the code base	2010-07-18 16:29:59 +00:00
queue/function/scattergather	Started path of deprecation of Sting's @Argument by splitting the annotation into @Output and @Input. Anything that's not an @Output should be an @Input.	2010-06-25 20:51:13 +00:00
utils	Refactoring the VCF writer code; now no longer uses VCFRecord or any of its related classes, instead writing directly to the writer. Integration tests pass, but some are actually broken and will be fixed this week.	2010-07-18 13:19:56 +00:00