hanna 199b43fcf2 Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a ... simplification of some of the locus traversal code. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2886 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-25 00:16:50 +00:00
..
arguments	Better handling of enums by the command-line argument system.	2010-01-20 21:36:46 +00:00
contexts	Support for reading in table of rsIDs -> dbSNP builds to back generate a dbSNP build X from a single file. Very useful indeed. dbSNP -> VC now captures the rsID in the context	2010-02-12 22:40:55 +00:00
datasources	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
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	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
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	Basic support for very simple index-driven locus traversals. Interface has been changed to	2010-01-29 03:14:26 +00:00
refdata	starting on RODs for Reads: made RODRecordList implement list<RODatum> (so we can sub in fake lists during testing), and removed unnecessary generic-ness. Removed BrokenRODSimulator, which isn't being used.	2010-02-24 22:11:53 +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	We were still dropping halves of some pairs, in which both reads were assigned to the same position. Fixed.	2010-02-24 23:13:23 +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