Eric Banks e7c35a907f Fixes to BQSR for the --maximum_cycle_value argument. ... - It's now written into the recal report so that it can be used in the PrintReads step. - Note that we also now write the --deletions_default_quality value which accidentally wasn't being written before! - Added tests to make sure that the value of the --maximum_cycle_value is being used properly by PR with -BQSR. (This is my last non-branch commit; all future pushes will follow new GATK practices)		2013-02-05 17:38:03 -05:00
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gatk	Fixes to BQSR for the --maximum_cycle_value argument.	2013-02-05 17:38:03 -05:00
utils	Moving the random number generator over to using GenomeAnalysisEngine.getRandomGenerator in the logless versus exact pair hmm unit test. We don't believe this will fix the problem with the non-deterministic test failures but it will give us more information the next time it fails.	2013-02-05 12:56:20 -05:00