ebanks 347608cfe0 remove hacked traversal in preparation for move to Matt's new one ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1091 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-25 14:32:05 +00:00
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datasources	Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude.	2009-06-23 23:48:06 +00:00
executive	Changed the duplicate traversal over to the new style of traversal and plumbed into the genome analysis engine. Also added a CountDuplicates walker, to validate the engine.	2009-06-22 21:11:18 +00:00
iterators	Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude.	2009-06-23 23:48:06 +00:00
refdata	Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.	2009-06-22 14:39:41 +00:00
traversals	remove hacked traversal in preparation for move to Matt's new one	2009-06-25 14:32:05 +00:00
walkers	remove hacked traversal in preparation for move to Matt's new one	2009-06-25 14:32:05 +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	Changed the duplicate traversal over to the new style of traversal and plumbed into the genome analysis engine. Also added a CountDuplicates walker, to validate the engine.	2009-06-22 21:11:18 +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
package.html	More package-level documentation.	2009-06-17 16:28:45 +00:00