Ryan Poplin f6905630bb Adding Unit test for Haplotype class. Used in HC's genotype given alleles mode.		2012-03-05 21:08:07 -05:00
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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	Getting rid of redundant methods in MathUtils. Adding unit tests for approximateLog10SumLog10 and normalizeFromLog10. Increasing the precision of the Jacobian approximation used by approximateLog10SumLog which changes the UG+HC integration tests ever so slightly.	2012-03-05 12:28:32 -05:00
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 test for Haplotype class. Used in HC's genotype given alleles mode.	2012-03-05 21:08:07 -05:00
BaseTest.java	ReadGroupProperties walker and associated infrastructure	2012-03-01 15:01:11 -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	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00