aaron db9570ae29 Looks bigger than it is: ... * Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes). * Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations. You can now specify: "-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2586 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-15 00:14:35 +00:00
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alignment	Misc bug fixes.	2010-01-05 14:48:19 +00:00
analyzecovariates	Fixed an issue with recalibrating original quality scores above Q40. There is a new option -maxQ which sets the maximum quality score possible for when a RecalDatum tries to compute its quality score from the mismatch rate. The same option was added to AnalyzeCovariates to help with plotting q scores above Q40. Added an integration test which makes use of this new -maxQ option.	2010-01-07 13:50:30 +00:00
gatk	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
oneoffprojects	two fixes in the new cached DbSNP code:	2010-01-13 00:27:34 +00:00
playground	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
utils	Looks bigger than it is:	2010-01-15 00:14:35 +00:00