Ryan Poplin b4e69239dd In order to be considered an informative read in the PerReadAlleleLikelihoodMap it has to be informative compared to all other alleles not just the worst allele. Also, fixing a bug when there is only one allele in the map.		2012-10-18 14:31:15 -04:00
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commandline	Refactored argument matching to support other plugins in addition to file lists.	2012-10-15 15:10:45 -04:00
gatk	In order to be considered an informative read in the PerReadAlleleLikelihoodMap it has to be informative compared to all other alleles not just the worst allele. Also, fixing a bug when there is only one allele in the map.	2012-10-18 14:31:15 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Refactor ExactCallLogger into a separate class	2012-10-16 13:30:09 -04:00
BaseTest.java	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Renaming -cnt to -nct for consistency	2012-09-05 21:13:19 -04:00