Mark DePristo 80a4ce0edf Bugfix for incorrect error messages for missing BAMs and VCFs ... -- Missing BAMs were appearing as StingExceptions -- Missing VCFs were showing up as CommandLineErrors, but it's clearer for them to be CouldNotReadInputFile exceptions -- Added integration tests to ensure missing BAMs, VCFs, and -L files are properly thrown as CouldNotReadInputFile exceptions -- Added path to standard b37 BAM to BaseTest -- Cleaned up code in SAMDataSource, removing my parallel loading code as this just didn't prove to be useful.		2012-01-23 09:52:07 -05:00
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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	Bug fix for VariantSummary	2012-01-05 21:51:06 -05:00
EngineFeaturesIntegrationTest.java	Bugfix for incorrect error messages for missing BAMs and VCFs	2012-01-23 09:52:07 -05:00
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