hanna 2a5be1debe Cleanup in datasources.providers namespace. Make it easier for others writing traversal engines to use. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@803 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-22 19:12:00 +00:00
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dataSources	Cleanup in datasources.providers namespace. Make it easier for others writing traversal engines to use.	2009-05-22 19:12:00 +00:00
executive	Better integration of reference-ordered data into the data sharding system.	2009-05-21 20:09:32 +00:00
iterators	Cleanup in datasources.providers namespace. Make it easier for others writing traversal engines to use.	2009-05-22 19:12:00 +00:00
refdata	Auxiliary class that can read one line from samtools pileup file. Used by rodSAMPileup to read pairs of lines as needed. NOTE: this class implements Genotype and (a trivial) GenotypeList, but it is NOT a rod!	2009-05-22 17:20:01 +00:00
traversals	Cleanup in datasources.providers namespace. Make it easier for others writing traversal engines to use.	2009-05-22 19:12:00 +00:00
walkers	For some reason the apostraphes in the comments were throwing annoying	2009-05-22 14:07:07 +00:00
CommandLineGATK.java	Catch and rethrow the walker's required argument, so that command-line arguments will be displayed when the GATK throws an argument exception.	2009-05-20 19:17:16 +00:00
GATKArgumentCollection.java	Integrate more feedback on command-line argument system. Focus on help	2009-05-20 19:01:25 +00:00
GenomeAnalysisEngine.java	@Required / @Allows flags for main arguments.	2009-05-19 23:26:17 +00:00
LocusContext.java	1. Added a by-interval traversal.	2009-04-24 04:33:35 +00:00
OutputTracker.java	N-way parallelism. Works for small test cases. Untested for large test cases.	2009-05-01 19:34:09 +00:00
Reads.java	Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along	2009-05-15 21:02:12 +00:00
WalkerManager.java	@Required / @Allows flags for main arguments.	2009-05-19 23:26:17 +00:00