kiran 48e311a5ea Added copyright notice. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3980 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-08 07:11:51 +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	Added a generic method for returning the complete command-line used when calling a walker, to be used in the bam/vcf headers. As requested, every possible engine/walker argument is included. I've added it to the Unified Genotyper output, so people can try it out and let me know what they think. Something that needs to be discussed in group meeting: what happens when we merge VCFs? Do we keep all of the command-lines?	2010-08-08 03:53:07 +00:00
gatk	Added copyright notice.	2010-08-08 07:11:51 +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/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	1) AlleleBalance is no longer a standard annotation, but the Allelic Depth (AD) is for each sample.	2010-08-06 12:05:14 +00:00