Eric Banks 10e74a71eb We now allow arbitrary annotations other than dbSNP (e.g. HM3) to come out of the Unified Genotyper. This was already set up in the Variant Annotator Engine and was just a matter of hooking UG up to it. Added integration test to ensure correct behavior.		2012-04-10 12:30:35 -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	We now allow arbitrary annotations other than dbSNP (e.g. HM3) to come out of the Unified Genotyper. This was already set up in the Variant Annotator Engine and was just a matter of hooking UG up to it. Added integration test to ensure correct behavior.	2012-04-10 12:30:35 -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	Adding unit tests for the very important log10sumLog10 util method.	2012-04-09 14:28:25 -04:00
BaseTest.java	Bug fix: BaseTest change shouldn't have been committed, first cleanup of SNP pool code (more to follow)	2012-04-03 18:55:52 -04:00
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