kiran fd20f5c2e8 For a file or files backed by a ROD implementing AllelicVariant, outputs a VCF file summarizing the information. Metadata like Hapmap and dbSNP membership, genotype LOD, read depth, etc, are annotated appropriately. The results output by this program are equivalent to those given by Gelis2PopSNPs.py. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1544 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-08 06:12:18 +00:00
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bwa	Checkpoint. The BWT that we generate now matches the first 16% of the BWT that BWT-SW generates. Cleaned up output streams to separate the byte packing / word packing from the data structure generation.	2009-09-02 22:18:17 +00:00
gatk	Lots of changes: (I'll send email out in a sec)	2009-09-07 01:12:09 +00:00
playground	For a file or files backed by a ROD implementing AllelicVariant, outputs a VCF file summarizing the information. Metadata like Hapmap and dbSNP membership, genotype LOD, read depth, etc, are annotated appropriately. The results output by this program are equivalent to those given by Gelis2PopSNPs.py.	2009-09-08 06:12:18 +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	Improvements to the CountCovariates and TableRecablirator, as well as regression tests for SLX and 454 data	2009-09-04 22:26:57 +00:00