depristo 8944800f60 Minor refactoring for Ryan ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3986 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-09 18:05:23 +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	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
commandline	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
gatk	Minor refactoring for Ryan	2010-08-09 18:05:23 +00:00
oneoffprojects	VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:	2010-08-05 18:47:53 +00:00
playground	Replaced by SelectVariants	2010-08-08 07:07:42 +00:00
queue	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
utils	providing a way to specify how you'd like -BTI combined with your -L options; set BTIMR to either UNION (default) or INTERSECTION.	2010-08-09 14:00:52 +00:00