aaron 782e0018e4 removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come. ... *** Three integration tests had to change: *** RecalibarationWalkersIntegrationTest: One of the tests was using the interval as the snp track, and wasn't supplying a DbSNP track (for CountCovariates) SequenomValidationConverterIntegrationTest: relies on Plink ROD which we've removed. PileupWalkerIntegrationTest: we no longer have implicit interval tracks, so there isn't a rod name over the specified region. Otherwise the same result. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4292 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-15 22:54:49 +00:00
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net/sf/picard/reference	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
org/broadinstitute/sting	removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come.	2010-09-15 22:54:49 +00:00