ebanks 4d4db7fe63 Renaming for consistency ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3049 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-19 18:45:01 +00:00
..
arguments	New sharding system is live. Disable with -ds.	2010-03-17 03:32:45 +00:00
contexts	Some significant changes to the annotator:	2010-03-18 05:38:32 +00:00
datasources	Set the eagerDecode flag in such a way that the binary data block in the BAM will always be considered dirty.	2010-03-16 22:01:23 +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	Rework the way the MicroScheduler handles locus shards to handle intervals that span shards	2010-03-11 18:40:31 +00:00
filters	oops, need to update class names too	2010-03-17 14:01:31 +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	Fixing/cleaning up the vcf merge util	2010-03-19 15:13:32 +00:00
traversals	Rework the way the MicroScheduler handles locus shards to handle intervals that span shards	2010-03-11 18:40:31 +00:00
walkers	Renaming for consistency	2010-03-19 18:45:01 +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	Khalid found an out-of-memory condition with the new sharding system when	2010-03-19 02:43:46 +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