ebanks 73a14a985b Moving VariantsToVCF to core. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3078 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-26 18:55:12 +00:00
..
arguments	New sharding system is live. Disable with -ds.	2010-03-17 03:32:45 +00:00
contexts	VariantFiltration can now filter specific samples.	2010-03-22 20:45:11 +00:00
datasources	New, much less memory intensive implementation of BAM file sharding. Streams indices together with the expectation	2010-03-25 17:41:22 +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	For Sarah Calvo: initial implementation of read pair traversal, for BAM files	2010-03-21 23:22:25 +00:00
filters	Minor bug workaround in GenotypeConcordance module (see todo). General platform read filter. You can say -rl Platform illumina to remove all SLX reads	2010-03-22 02:47:09 +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	HapMap-to-VCF now works fine within Variants-to-VCF. Added integration test for it and removed old code.	2010-03-26 18:34:59 +00:00
traversals	For Sarah Calvo: initial implementation of read pair traversal, for BAM files	2010-03-21 23:22:25 +00:00
walkers	Moving VariantsToVCF to core.	2010-03-26 18:55:12 +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	New sharding system is going live again for on-the-fly merging.	2010-03-25 18:39:04 +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