Eric Banks 41068b6985 The commit constitutes a major refactoring of the UG as far as the genotype likelihoods are concerned. I hate to do this in stable, but the VCFs currently being produced by the UG are totally busted. I am trying to make just the necessary changes in stable, doing everything else in unstable later. Now all GL calculations are unified into the GenotypeLikelihoods class - please try and use this functionality from now on instead of duplicating the code.		2012-03-15 16:08:58 -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	The commit constitutes a major refactoring of the UG as far as the genotype likelihoods are concerned. I hate to do this in stable, but the VCFs currently being produced by the UG are totally busted. I am trying to make just the necessary changes in stable, doing everything else in unstable later. Now all GL calculations are unified into the GenotypeLikelihoods class - please try and use this functionality from now on instead of duplicating the code.	2012-03-15 16:08:58 -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	The commit constitutes a major refactoring of the UG as far as the genotype likelihoods are concerned. I hate to do this in stable, but the VCFs currently being produced by the UG are totally busted. I am trying to make just the necessary changes in stable, doing everything else in unstable later. Now all GL calculations are unified into the GenotypeLikelihoods class - please try and use this functionality from now on instead of duplicating the code.	2012-03-15 16:08:58 -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