Khalid Shakir b8b7f28aa9 Revving Picard to pick up new SamFileHeaderMerger. ... Updated ReadFilter abstract class to implement (via UnsupportedOperationException) the new SamRecordFilter.filterOut(). In IndelRealignerIntegrationTest updates for Picard fixes to SAMRecord.getInferredInsertSize() in svn r1115 & r1124. - Ran FixMates to create new input BAM since running IR with variable maxReadsInMemory means all reads weren't realigned leading to different outputs. - Updated md5s to match new expectations after looking at TLEN diff engine output.		2012-05-02 16:47:28 -04:00
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datasources	Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped	2012-04-27 09:58:38 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Taking care of bad cigars in the GATK	2012-03-20 14:32:57 -04:00
iterators	Removing extended event related unit tests	2012-04-02 14:40:36 -04:00
refdata	Merge with master	2011-11-19 09:56:06 -05:00
report	AggregateMetrics:	2012-04-17 11:45:32 -04:00
samples	Added function to get founders IDs in SampleDB	2012-04-25 12:49:36 -04:00
traversals	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
walkers	Revving Picard to pick up new SamFileHeaderMerger.	2012-05-02 16:47:28 -04:00
EngineFeaturesIntegrationTest.java	More extensive testing of type of error thrown in multi-threaded walker test	2012-04-13 09:23:33 -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