kshakir 798178b167 Another case of just because you can do something doesn't mean you should. ... Scala type inference for the implicit return types on implicit methods was a little too much for poor IntelliJ IDEA to handle, and it was breaking things like copy/paste, auto-complete, etc. Also updated the Queue package to include all Sting utils. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5646 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-15 15:39:56 +00:00
..
Aligner.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
AnalyzeCovariates.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
CreatePackager.xsl	Adding the native jna support libraries from the jna.jar to the Queue package jar.	2011-01-08 10:48:30 +00:00
FindContaminatingReadGroups.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
GATK-Picard.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
GATKEngine.xml	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
GATKResources.xml	/broad/1KG doesn't exist	2010-10-06 12:54:38 +00:00
GenomeAnalysisTK.xml	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
IndelGenotyper.xml	Bringing IndelGenotyper back to life	2010-02-03 20:12:49 +00:00
LocalRealignmentAroundIndels.xml	Since IntervalCleaner is gone for good, it is sensible to update the package to refer to the new IndelRealigner instead	2010-02-24 16:42:56 +00:00
PicardPrivate.xml	Update to the latest rev of the picard sharding patch. Includes updates reflecting	2010-06-06 20:33:21 +00:00
QualityScoresRecalibration.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
Queue.xml	Another case of just because you can do something doesn't mean you should.	2011-04-15 15:39:56 +00:00
RMDIndexer.xml	include the codecs into the RMD indexer that are available in the GATK, not just Tribble	2010-11-11 06:35:04 +00:00
UnifiedGenotyper.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
VariantAnnotator.xml	Include all standard annotations	2010-10-11 20:52:08 +00:00
VariantEval.xml	Add CountFunctionalVariants to local release (for firehose)	2010-07-17 01:36:16 +00:00
VariantFiltration.xml	Temporary solution: add the commons logging implementation to the VariantFiltration package. Downstream solution is described in GSA-262.	2010-01-23 01:46:18 +00:00
VariantRecalibration.xml	VariantOptimizer package is moved to core, renamed as VariantRecalibration, and added to the binary release package. VariantOptimizer walker is renamed to GenerateVariantClustersWalker and ApplyVariantClustersWalker renamed to VariantRecalibrator. Integration tests added, performance tests still to be done.	2010-05-28 18:20:18 +00:00