droazen a5acb0b7a6 Fix for bug GSA-314: Detect -XL and -L incompatibility. An ArgumentException is ... now thrown if the combination of -L and -XL intervals specified on the command line results in an empty interval set after set subtraction. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5571 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-04 18:41:55 +00:00
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arguments	A significant refactoring of the ROD system, done largely to simplify the process of	2010-12-31 04:52:22 +00:00
contexts/variantcontext	Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.	2010-12-08 17:22:29 +00:00
datasources	Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately.	2011-03-29 21:04:09 +00:00
executive	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
iterators	More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated	2011-03-03 03:55:24 +00:00
refdata	Oops...forgot to commit the changes that allow primitive VCF streaming.	2011-01-12 21:54:51 +00:00
traversals	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +00:00
walkers	Updated to now longer include 2nd-best base output	2011-04-03 20:13:10 +00:00
CommandLineExecutableUnitTest.java	Fix for bug GSA-441: BAM file list with blank lines gives a confusing error	2011-04-01 15:04:35 +00:00
GenomeAnalysisEngineUnitTest.java	Fix for bug GSA-314: Detect -XL and -L incompatibility. An ArgumentException is	2011-04-04 18:41:55 +00:00
WalkerManagerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00