Mauricio Carneiro 77a03c9709 Patching special case in the adaptor clipping ... * if the adaptor boundary is more than MAXIMUM_ADAPTOR_SIZE bases away from the read, then let's not clip anything and consider the fragment to be undetermined for this read pair. * updated md5's accordingly		2012-01-11 17:47:44 -05:00
..
datasources	Better file count / buffering variation in test suite. Parameterized read shard buffering. Misc cleanup.	2011-12-06 10:10:38 -05:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
iterators	Better file count / buffering variation in test suite. Parameterized read shard buffering. Misc cleanup.	2011-12-06 10:10:38 -05:00
refdata	Merge with master	2011-11-19 09:56:06 -05:00
report	Right aligning GATKReport numeric columns and updated MD5s in tests.	2011-12-05 23:22:15 -05:00
samples	Added UnitTests for getFamilies() and getChildrenWithParents()	2011-12-09 15:57:07 +01:00
traversals	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
walkers	Patching special case in the adaptor clipping	2012-01-11 17:47:44 -05:00
EngineFeaturesIntegrationTest.java	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -04:00
GenomeAnalysisEngineUnitTest.java	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00