aaron e682460c1f add a fix so that XL arguments won't cancel out -BTI arguments, fixed a bug for Ben where the ROD -> interval list conversion was throwing an exception, and some old code removal. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3174 348d0f76-0448-11de-a6fe-93d51630548a		2010-04-15 16:31:43 +00:00
..
arguments	Refactoring intervals, separating the process of parsing interval lists,	2010-04-13 15:50:38 +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	Added AnnotatorROD - the TabularROD format specific to GenomicAnnotator	2010-04-14 14:39:50 +00:00
traversals	Fare thee well, oh LocusWindowTraversal.	2010-03-29 13:17:26 +00:00
walkers	Changed a variable name	2010-04-14 14:38:18 +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	add a fix so that XL arguments won't cancel out -BTI arguments, fixed a bug for Ben where the ROD -> interval list conversion was throwing an exception, and some old code removal.	2010-04-15 16:31:43 +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