ebanks 5c35be39ef Now that extended events work for reference traversals, turn it off in the genotyper for non-indel models (thereby fixing busted integration tests). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2974 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-10 03:14:06 +00:00
..
arguments	Better handling of enums by the command-line argument system.	2010-01-20 21:36:46 +00:00
contexts	Alleles now hash correctly.	2010-03-09 18:09:44 +00:00
datasources	In reference traversals, this view did not expect a possibility of TWO alignment contexts (base pileup followed by extended event pileup) associated with the same location. As the result, extended event pileups were silently skipped even when enabled in the traversal engine. Fixed.	2010-03-09 22:18:44 +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	Partially reclaim performance lost during integration test fixes.	2010-03-09 12:36:11 +00:00
filters	Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark.	2010-01-03 21:31:04 +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	Alleles now hash correctly.	2010-03-09 18:09:44 +00:00
traversals	Fix bug that's been in the GATK for a very long time: update nReads (as well	2010-03-08 22:44:54 +00:00
walkers	Now that extended events work for reference traversals, turn it off in the genotyper for non-indel models (thereby fixing busted integration tests).	2010-03-10 03:14:06 +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	A few stopgap fixes to get the GATK to the point where the old sharding	2010-03-07 21:01:25 +00:00
Reads.java	changes to intelligently log overflowing locus pile-ups.	2010-01-20 08:09:48 +00:00
WalkerManager.java	Bug fix for help text / version number - help text retriever was crashing in the debugger if help text hadn't been built.	2010-01-20 19:18:19 +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