depristo 8e9e2f4502 Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@716 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-14 21:06:28 +00:00
..
dataSources	Oops. Forgot to add new file to svn.	2009-05-14 00:52:30 +00:00
executive	Switched dependencies of GenomeAnalysisTK to depend on GenomeAnalysisEngine.	2009-05-11 22:33:00 +00:00
iterators	Moved the iterators over to the StingSAMIterator interface. This will help us ensure that iterators that need to be closed get closed.	2009-05-14 16:52:18 +00:00
refdata	Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.	2009-05-14 21:06:28 +00:00
traversals	Fixing the naming of the function I checked in earlier.	2009-05-14 19:27:10 +00:00
walkers	intervals_file + genome_loc => intervals.	2009-05-12 01:04:18 +00:00
CommandLineGATK.java	The GATK doesn't need the rest	2009-05-14 16:20:45 +00:00
GATKArgumentCollection.java	Added code to correct the violation of the parsing interface. Now the analysis type resides in the command line arg, but is stored into the argument collection before it's passed to the genomeAnalysisEngine.	2009-05-12 15:33:55 +00:00
GenomeAnalysisEngine.java	Added a getter for command-line arguments.	2009-05-14 13:55:52 +00:00
LocusContext.java	1. Added a by-interval traversal.	2009-04-24 04:33:35 +00:00
OutputTracker.java	N-way parallelism. Works for small test cases. Untested for large test cases.	2009-05-01 19:34:09 +00:00
WalkerManager.java	Refactor common functionality out of WalkerManager and into JVMUtils and PathUtils. Add support for loading walkers from a jar.	2009-03-30 23:20:55 +00:00