Mauricio Carneiro 68d0211fa1 Improved BQSR plotting and some new parameters ... * Refactored CycleCovariate to be a fragment covariate instead of a per read covariate * Refactored the CycleCovariateUnitTest to test the pairing information * Updated BQSR Integration tests accordingly * Made quantization levels parameter not hidden anymore * Added hidden option to keep intermediate plotting files for debug purposes (they're automatically deleted) * Added hidden option not to generate the plots automatically (important for scatter/gathering)		2012-04-19 09:31:41 -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	Improved BQSR plotting and some new parameters	2012-04-19 09:31:41 -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	minor misc optimizations to PairHMM	2012-04-18 15:02:26 -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	New way to handle exceptions in multi-threaded GATK	2012-04-13 09:23:33 -04:00