aaron 86dc98bfb5 update the documentation for CombineDuplicates for the new help system. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2324 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-11 17:01:42 +00:00
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contexts	Generalized the StratifiedAlignmentContext code so that it's easy to add new ways to stratify. Then added an MQ0-free stratification so we don't need to be carrying around 2 different alignment contexts (full vs. mq0-free) anymore.	2009-12-10 19:50:06 +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	Fix obvious cut/paste error in output stream management code.	2009-12-10 19:23:13 +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	update the documentation for CombineDuplicates for the new help system.	2009-12-11 17:01:42 +00:00
walkers	documentation updates for the new help system.	2009-12-11 16:15:44 +00:00
CommandLineExecutable.java	Command-line arguments for SamReadFilters.	2009-11-10 23:36:17 +00:00
CommandLineGATK.java	Only show extra walker help if the user didn't specify a walker or specified	2009-12-10 16:43:06 +00:00
GATKArgumentCollection.java	Un-reinventing the wheel. --sleep argument removed.	2009-12-02 20:19:28 +00:00
GenomeAnalysisEngine.java	Before, we were only checking that the reference was present if @Requires required that a reference was present. Now we always check that a reference is present, so that we get an intelligent error message.	2009-12-10 19:15:48 +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