hanna 30eb28886b Basic functionality for intervaled reads in new sharding system. Not currently filtering out cruft, so ... the mode of operation is currently queryOverlapping rather than queryContained. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2899 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-26 21:41:55 +00:00
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arguments	Better handling of enums by the command-line argument system.	2010-01-20 21:36:46 +00:00
contexts	This commit is for Kiran	2010-02-26 18:18:38 +00:00
datasources	Basic functionality for intervaled reads in new sharding system. Not currently filtering out cruft, so	2010-02-26 21:41:55 +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	Basic functionality for intervaled reads in new sharding system. Not currently filtering out cruft, so	2010-02-26 21:41:55 +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	Better handling of enums by the command-line argument system.	2010-01-20 21:36:46 +00:00
iterators	Clean up the code a bit following the introduction of reduceByInterval.	2010-02-25 01:20:22 +00:00
refdata	Support for no qual fields in VCF; better support for Mendelian violation calculations	2010-02-26 00:29:17 +00:00
traversals	Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a	2010-02-25 00:16:50 +00:00
walkers	RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother.	2010-02-25 22:48:55 +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	Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a	2010-02-25 00:16:50 +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