ebanks 032d0436e6 Added ROD for 1KG SNP calls ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@988 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-11 19:53:51 +00:00
..
datasources	Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.	2009-06-11 18:13:22 +00:00
executive	Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.	2009-06-11 18:13:22 +00:00
iterators	Bumped picard to latest svn version.	2009-06-10 14:36:34 +00:00
refdata	Added ROD for 1KG SNP calls	2009-06-11 19:53:51 +00:00
traversals	Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.	2009-06-11 18:13:22 +00:00
walkers	Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does *not* affect the default functionality of the standard PileupWalker	2009-06-10 17:31:00 +00:00
CommandLineExecutable.java	initial check-in of an easy way to create command line tools based on the GATK	2009-06-10 17:34:02 +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	checked in a sample xml file used to store the defaults for the SomaticCoverage tool, and added it to the SomaticCoverage.jar in build.sml. Also added a inputStream marshalling method to the GATKArgumentCollection.	2009-06-10 20:46:16 +00:00
GenomeAnalysisEngine.java	Pooling resources to lower memory consumption.	2009-06-10 13:39:32 +00:00
LocusContext.java	Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...	2009-05-28 20:13:01 +00:00
OutputTracker.java	Lazy creation of output streams. Only create output streams when absolutely necessary.	2009-05-26 21:56:57 +00:00
Reads.java	Pooling resources to lower memory consumption.	2009-06-10 13:39:32 +00:00
WalkerManager.java	Farewell, functionalj. You promised much, but you could not deliver.	2009-05-28 01:35:49 +00:00