droazen d650efd40a Fix for bug GSA-449: Intervals that are not in GATK format are not validated ... to the same standard as GATK format intervals. Full validation against contig bounds is now performed for all intervals, regardless of their source. Also fixed a few tests for validation exclusions that were backwards. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5698 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-27 18:12:10 +00:00
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alignment	Quick fix for Danny Lieber: flesh out the additional functionality required	2011-01-31 05:28:37 +00:00
commandline	Fixed long-standing bug reported by Mauricio where @Arguments assigned to	2011-01-12 22:18:24 +00:00
datasources/pipeline	Removed deprecated getDbsnpFile.	2011-02-08 21:12:15 +00:00
gatk	Fix for bug GSA-449: Intervals that are not in GATK format are not validated	2011-04-27 18:12:10 +00:00
jna	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
oneoffprojects/walkers	Removing broken imports (boo)	2011-04-26 18:55:25 +00:00
playground/gatk/walkers	UnifiedGenotyper now BAQs via ADD_TAG to facilitate using BAQed quals for GL calculations but unBAQed quals for annotation calculations. UnifiedGenotyper now produces SNP and indel calls simultaneously. 40 base mismatch intrinsic filter removed from UG to greatly simplify the code. RankSumTests are now standard annotations but the integration tests are commented out pending changes that will allow random annotations to work.	2011-04-06 19:06:24 +00:00
utils	Refactored IntervalUtils used to parse and scatter intervals for Queue.	2011-04-26 00:06:00 +00:00
BaseTest.java	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
StingTextReporter.java	Cleanup testng listener configuration.	2010-11-15 23:43:14 +00:00
WalkerTest.java	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00