kshakir 33400074fa Updated tribble BED parsing code to use the official UCSC spec, and updated tests to match expected results. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4188 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-01 21:49:06 +00:00
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CallableLociWalkerIntegrationTest.java	GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line	2010-06-02 22:26:32 +00:00
CompareCallableLociWalkerIntegrationTest.java	Updated tribble BED parsing code to use the official UCSC spec, and updated tests to match expected results.	2010-09-01 21:49:06 +00:00
DepthOfCoverageB36IntegrationTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
DepthOfCoverageIntegrationTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00