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gatk-3.8/java/src/edu/mit/broad/sting/atk
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jmaguire 716af47dd5 Added NullWalker module (do nothing). 
Added SingleSampleGenotyper module (old-school single sample genotyping).

Added Utils.SortPermutation (return the permutaton that would sort the input array).
Added Utils.PermuteArray (apply a permutation to an array).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@29 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-03-10 21:26:07 +00:00
..
modules Added NullWalker module (do nothing). 2009-03-10 21:26:07 +00:00
AnalysisTK.java Added NullWalker module (do nothing). 2009-03-10 21:26:07 +00:00
LocusContext.java Clean up 3rd party dependencies. 2009-03-10 19:34:00 +00:00
LocusIterator.java Clean up 3rd party dependencies. 2009-03-10 19:34:00 +00:00
LocusWalker.java Phase II support for generic reference order data set parsing. 2009-02-28 20:47:48 +00:00
PrepareROD.java Clean up 3rd party dependencies. 2009-03-10 19:34:00 +00:00
ReadWalker.java Clean up 3rd party dependencies. 2009-03-10 19:34:00 +00:00
TraversalEngine.java Clean up 3rd party dependencies. 2009-03-10 19:34:00 +00:00