ebanks 2520889cb3 Check for bad intervals and don't emit them ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2849 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-16 21:42:36 +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	Got back most of the performance lost when I fixed the dropped reads problem.	2010-02-12 19:59:56 +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 support for very simple index-driven locus traversals. Interface has been changed to	2010-01-29 03:14:26 +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	should never commit without running intergration tests.	2010-02-12 23:42:37 +00:00
traversals	VariantEval2 test framework implemented; Kiran is experimenting with the system. Not for use by anyone else. VariantContext appears to work well; I'll release it next week for general use following docs of the functions. Removing newvarianteval and other classes to avoid any future confusion. Update to TraverseLoci and RodLocusView to simplify a few functions and to correct some minor errors. All tests pass without modification.	2010-01-30 20:51:24 +00:00
walkers	Check for bad intervals and don't emit them	2010-02-16 21:42:36 +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	Various improvements and fixes:	2010-02-07 04:21:04 +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