Mark DePristo 7c5cdb51c2 UnitTests for ActivityProfile and minor ART cleanup ... -- TODO for ryan -- there are bugs in ActivityProfile code that I cannot fix right now :-( -- UnitTesting framework for ActivityProfile -- needs to be expanded -- Minor helper functions for ActiveRegion to help with unit tests		2012-03-14 17:26:37 -04:00
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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	CountReadsInActiveRegions now emits a detailed GATK report	2012-03-14 17:26:37 -04:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	UnitTests for ActivityProfile and minor ART cleanup	2012-03-14 17:26:37 -04:00
BaseTest.java	CalibrateGenotypeLikelihoods now emits the position of the variant for debugging	2012-03-09 16:00:07 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
MedianUnitTest.java	Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.	2012-03-05 08:28:42 -05:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00