ebanks 303972aa4b Yup, I broke the build... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1750 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-30 20:20:43 +00:00
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alignment	Support negative strand alignments.	2009-09-30 18:10:26 +00:00
gatk	Yup, I broke the build...	2009-09-30 20:20:43 +00:00
playground	Adjusted Genotype concordance to more accurately use the new Genotyping code, fixed the VCF rod, and temp. fix the build by reintroducing Shermans ReadCigarFormatter	2009-09-29 21:28:21 +00:00
secondarybase	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
utils	Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.	2009-09-29 22:23:19 +00:00