aaron f5cba5a6bb Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1132 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-30 19:17:24 +00:00
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datasources	Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.	2009-06-30 19:17:24 +00:00
executive	TraverseByLocusWindow -- asstd bug fixes.	2009-06-25 22:51:38 +00:00
iterators	Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.	2009-06-30 19:17:24 +00:00
refdata	Added a ROD (SangerSNP) for parsing the Sanger's chr20 pilot1 SNP calls.	2009-06-29 16:32:12 +00:00
traversals	Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.	2009-06-30 19:17:24 +00:00
walkers	Read groups are now sorted in the output data, for convenience	2009-06-30 16:50:44 +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	First pass at passing lists of files / lists of interval arguments work. Note that the interval	2009-06-25 20:44:23 +00:00
GenomeAnalysisEngine.java	TraverseByLocusWindow -- asstd bug fixes.	2009-06-25 22:51:38 +00:00
LocusContext.java	Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.	2009-06-30 19:17:24 +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
package.html	More package-level documentation.	2009-06-17 16:28:45 +00:00