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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ReferenceOrderedDataPoolUnitTest.java	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
SAMBAMDataSourceUnitTest.java	Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax	2010-08-25 03:47:57 +00:00