ebanks 5fab934f4e - moved the reference maker to its own directory ... - added first version of a more complicated reference maker which takes in RODs and creates an alternative reference based on the variants (indels and/or SNPs) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1409 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-11 18:01:06 +00:00
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examples	Update naming for consistency.	2009-06-30 22:03:21 +00:00
gatk	- moved the reference maker to its own directory	2009-08-11 18:01:06 +00:00
indels	change paths to new ones	2009-07-24 07:28:43 +00:00
piecemealannotator	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
somaticcoverage	Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists.	2009-07-21 18:50:51 +00:00
tools	A standalone picard-level tool for breaking individual reads into "pairs" of first/last N bases. Supports:	2009-08-10 20:42:49 +00:00
utils	RemapAlignments is a standalone picard-level tool that does not use gatk engine; moved to 'tools'	2009-08-10 15:41:07 +00:00