Khalid Shakir 91cb654791 AggregateMetrics: ... - By porting from jython to java now accessible to Queue via automatic extension generation. - Better handling for problematic sample names by using PicardAggregationUtils. GATKReportTable looks up keys using arrays instead of dot-separated strings, which is useful when a sample has a period in the name. CombineVariants has option to suppress the header with the command line, which is now invoked during VCF gathering. Added SelectHeaders walker for filtering headers for dbGAP submission. Generated command line for read filters now correctly prefixes the argument name as --read_filter instead of -read_filter. Latest WholeGenomePipeline. Other minor cleanup to utility methods.		2012-04-17 11:45:32 -04:00
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datasources	Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.	2012-04-02 14:27:36 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Taking care of bad cigars in the GATK	2012-03-20 14:32:57 -04:00
iterators	Removing extended event related unit tests	2012-04-02 14:40:36 -04:00
refdata	Merge with master	2011-11-19 09:56:06 -05:00
report	AggregateMetrics:	2012-04-17 11:45:32 -04:00
samples	Added UnitTests for getFamilies() and getChildrenWithParents()	2011-12-09 15:57:07 +01:00
traversals	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
walkers	Update VE IT to reflect new fields and bugfixes	2012-04-13 17:00:37 -04:00
EngineFeaturesIntegrationTest.java	More extensive testing of type of error thrown in multi-threaded walker test	2012-04-13 09:23:33 -04:00
GenomeAnalysisEngineUnitTest.java	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00