David Roazen 07b369ca7e Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package ... This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.		2012-12-19 10:25:22 -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	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	oops	2012-12-18 19:03:12 -05:00
walkers	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -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