ebanks f7c44ad019 - Read in arguments for the header based on reflection ... - Hook up Variation and Genotype in SSG git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2300 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-09 21:35:33 +00:00
..
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	- Read in arguments for the header based on reflection	2009-12-09 21:35:33 +00:00
CommandLineExecutable.java	Command-line arguments for SamReadFilters.	2009-11-10 23:36:17 +00:00
CommandLineGATK.java	Better handling of nulls output by	2009-12-09 19:34:56 +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	Refactoring of prior commit: better handling of unnamed package within the help system.	2009-12-09 20:12:35 +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