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gatk-3.8/java/src/org/broadinstitute/sting/gatk
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aaron 6e69193e3c Deprecated calls to getSamReader on both the GenomeAnalysisEngine and the TraversalEngine. This call fails in the new style traversals, but it won't disapear until the cut-over to the new traversals is complete. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@671 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-05-12 18:52:42 +00:00
..
dataSources LocusIterator iterated through LocusContexts, which was fine until now when we need something 2009-05-12 13:54:57 +00:00
executive Switched dependencies of GenomeAnalysisTK to depend on GenomeAnalysisEngine. 2009-05-11 22:33:00 +00:00
iterators LocusIterator iterated through LocusContexts, which was fine until now when we need something 2009-05-12 13:54:57 +00:00
refdata Reference-ordered data relies on bugs in the old command-line argument system to work. Update the ROD system to from -B track1 type1 file1 track2 type2 file2 to -B track1,type1,file1 -B track2,type2,file2. 2009-05-08 15:28:19 +00:00
traversals Deprecated calls to getSamReader on both the GenomeAnalysisEngine and the TraversalEngine. This call fails in the new style traversals, but it won't disapear until the cut-over to the new traversals is complete. 2009-05-12 18:52:42 +00:00
walkers intervals_file + genome_loc => intervals. 2009-05-12 01:04:18 +00:00
CommandLineGATK.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
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 Deprecated calls to getSamReader on both the GenomeAnalysisEngine and the TraversalEngine. This call fails in the new style traversals, but it won't disapear until the cut-over to the new traversals is complete. 2009-05-12 18:52:42 +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