aaron 8017fb123f changed the depth of coverage walkers class name, and added a dependency in the packaging system so that RODs will all get imported. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3116 348d0f76-0448-11de-a6fe-93d51630548a		2010-04-02 20:55:19 +00:00
..
arguments	fixing an annotation that was breaking the error log output system.	2010-03-30 15:34:04 +00:00
contexts	Minor useful changes to BaseUtils and MathUtils to support a new haplotype score annotation that determines to the two most likely haplotypes over an interval and scores variants by their consistency with a diploid model. Appears to be useful.	2010-03-28 21:45:22 +00:00
datasources	the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.	2010-03-31 22:39:56 +00:00
examples	Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes	2010-02-05 21:47:54 +00:00
executive	Fare thee well, oh LocusWindowTraversal.	2010-03-29 13:17:26 +00:00
filters	Filter lists can now end with .list or .txt.	2010-03-27 17:41:24 +00:00
io	Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.	2010-03-09 03:41:07 +00:00
iterators	In the new sharding system, if no read group is present, hallucinate one. Added	2010-03-07 23:01:34 +00:00
refdata	Reorganizing the way interval arguments are processed	2010-04-01 12:47:48 +00:00
traversals	Fare thee well, oh LocusWindowTraversal.	2010-03-29 13:17:26 +00:00
walkers	changed the depth of coverage walkers class name, and added a dependency in the packaging system so that RODs will all get imported.	2010-04-02 20:55:19 +00:00
CommandLineExecutable.java	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
CommandLineGATK.java	Update our error messages to point to getsatisfaction.com/gsa.	2010-01-27 19:16:28 +00:00
GenomeAnalysisEngine.java	Reorganizing the way interval arguments are processed	2010-04-01 12:47:48 +00:00
Reads.java	changes to intelligently log overflowing locus pile-ups.	2010-01-20 08:09:48 +00:00
WalkerManager.java	the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.	2010-03-31 22:39:56 +00:00
package-info.java	Put a major.minor version into the GATK Javadoc for reading. Also,	2010-01-15 21:48:30 +00:00