Eric Banks e93ff3ea6e Let's go back to having the SB/SLOD NOT computed by default. If you recall, it was only enabled by default because we thought we were going to use it when we made VQSR use random forests. But since we decided not to change VQSR, there's no reason to triple the computation for every variant site anymore.		2012-10-25 12:45:23 -04:00
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datasources	ExperimentalReadShardBalancerUnitTest was being skipped; fixed	2012-09-22 01:56:39 -04:00
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	Experimental, downsampler-friendly read shard balancer	2012-09-21 22:17:58 -04:00
refdata	Part I of GSA-462: Consistent RODBinding access across Ref and Read trackers	2012-08-30 10:15:10 -04:00
report	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
samples	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
traversals	Retiring TraverseReads and TraverseLoci after testing confirms nano scheduler version in single threaded version is fine	2012-10-22 16:55:06 -04:00
walkers	Let's go back to having the SB/SLOD NOT computed by default. If you recall, it was only enabled by default because we thought we were going to use it when we made VQSR use random forests. But since we decided not to change VQSR, there's no reason to triple the computation for every variant site anymore.	2012-10-25 12:45:23 -04:00
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	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
WalkerManagerUnitTest.java	Fixing walker unit test with the new naming convention	2012-07-20 17:50:29 -04:00