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
..
arguments	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
datasources	more fixes for the empty interval list problem; you can now run LocusWindow traversals with an empty interval list, but the GATK will give you a warning (unless you're running in unsafe mode).	2010-01-12 18:47:43 +00:00
executive	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
io	Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.	2009-09-16 08:33:56 +00:00
iterators	moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.	2009-12-29 07:40:48 +00:00
refdata	moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.	2009-12-29 07:40:48 +00:00
traversals	moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.	2009-12-29 07:40:48 +00:00
walkers	Fixing the testOtherOutput UG integration test so it will run.	2010-01-14 13:40:14 +00:00