Eric Banks 5c5d8e7cd3 Minor: cleaner way of turning off index-on-the-fly checking in case we want to turn it back on.		2012-03-18 00:53:29 -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	Rewriting a few of the indel integration tests for multi-allelics. The old tests were running b37 calls against a b36 reference, so the calls were all ref. The new tests are run against the pilot1 data and then those calls are fed back into the the same bam to test genotype given alleles, with a sprinkling of bi- and tri-allelics.	2012-03-16 14:21:27 -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	Add a conversion from the deprecated PL ordering to the new one. We need this for the DiploidSNPGenotypeLikelihoods which still use the old ordering. My intention is for this to be a temporary patch, but changing the ordering in DiploidSNPGenotypeLikelihoods is not appriopriate for committing to stable as it will break all of the external tools (e.g. MuTec) that are built on top of the class. We will have to talk to e.g. Kristian to see how disruptive this will be. Added unit tests to the GL conversions and indexing.	2012-03-16 11:14:37 -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	Minor: cleaner way of turning off index-on-the-fly checking in case we want to turn it back on.	2012-03-18 00:53:29 -04:00