Eric Banks b099e2b4ae Moving integration tests to protected		2013-01-08 09:34:08 -05:00
..
datasources	Use the new downsampling implementation by default	2012-12-10 09:44:50 -05:00
downsampling	Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"	2012-09-10 15:52:39 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
iterators	Use the new downsampling implementation by default	2012-12-10 09:44:50 -05:00
refdata	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
report	Removed sorting by row from walkers	2013-01-04 11:52:33 -05:00
samples	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
traversals	Archive the experimental Active Region Traversals	2013-01-04 17:05:31 -05:00
walkers	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
CommandLineGATKUnitTest.java	Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us.	2012-07-18 21:48:58 -04:00
EngineFeaturesIntegrationTest.java	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00
GenomeAnalysisEngineUnitTest.java	Moved (nearly) all Walkers from public to protected and removed GATKLite utils	2013-01-07 14:42:40 -05:00
MaxRuntimeIntegrationTest.java	Add GATK-wide command line argument to control the maximum runtime allowed for the GATK	2012-10-26 13:18:34 -04:00
WalkerManagerUnitTest.java	Fixing walker unit test with the new naming convention	2012-07-20 17:50:29 -04:00