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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Mark DePristo c8a06e53c1 DoC now properly handles reference N bases + misc. additional cleanups 
-- DoC now by default ignores bases with reference Ns, so these are not included in the coverage calculations at any stage.
-- Added option --includeRefNSites that will include them in the calculation
-- Added integration tests that ensures the per base tables (and so all subsequent calculations) work with and without reference N bases included
-- Reorganized command line options, tagging advanced options with @Advanced
 		2012-02-25 11:32:50 -05:00
..
datasources On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live. 2012-02-13 12:35:09 -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 On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live. 2012-02-13 12:35:09 -05:00
refdata Merge with master 2011-11-19 09:56:06 -05:00
report Revert "First implementation of GATKReportGatherer" 2012-02-08 23:28:55 -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 DoC now properly handles reference N bases + misc. additional cleanups 2012-02-25 11:32:50 -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