Joel Thibault 47e620dfbc Create BAM index to test shard boundaries		2013-01-03 17:00:12 -05:00
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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	Added unit test for outputting sorted GATKReport Tables	2013-01-03 16:53:59 -05:00
samples	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
traversals	Create BAM index to test shard boundaries	2013-01-03 17:00:12 -05:00
walkers	QD is now divided by the average length of the alternate allele (weighted by the allele count). The average length is stored in a related annotation, "AAL", which can be used to re-compute the "old" QD by simple multiplication. Integration tests *should* all pass.	2013-01-02 14:41:29 -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	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
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