ebanks 40c2d7a4bc Fix all-bases-mode and genotype-mode in the UG and add integration tests for them. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2295 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-09 17:41:30 +00:00
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contexts	fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview	2009-12-02 15:41:35 +00:00
datasources	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00
examples	- Optimized implementation of -byReadGroup in DoCWalker	2009-12-02 03:39:24 +00:00
executive	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00
filters	Added DuplicateReadFilter to filter out reads that are marked as duplicates.	2009-12-09 15:42:53 +00:00
io	Support for initialize() and onTraversalDone() output from parallelized walkers.	2009-10-26 20:18:31 +00:00
iterators	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00
refdata	Stage 3 of Variation refactoring:	2009-12-08 21:43:28 +00:00
traversals	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00
walkers	Fix all-bases-mode and genotype-mode in the UG and add integration tests for them.	2009-12-09 17:41:30 +00:00
CommandLineExecutable.java	Command-line arguments for SamReadFilters.	2009-11-10 23:36:17 +00:00
CommandLineGATK.java	Clean up some of the walker help output based on additional experience and	2009-12-07 21:33:11 +00:00
GATKArgumentCollection.java	Un-reinventing the wheel. --sleep argument removed.	2009-12-02 20:19:28 +00:00
GenomeAnalysisEngine.java	First pass at a reorganized walker info display. Groups walkers by package	2009-12-04 23:24:29 +00:00
Reads.java	Command-line arguments for SamReadFilters.	2009-11-10 23:36:17 +00:00
WalkerManager.java	Move some files around to reflect our growing help infrastructure.	2009-12-07 19:23:12 +00:00
package-info.java	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00