Geraldine Van der Auwera 61349ecefa Cleaned up annotations ... - Moved AverageAltAlleleLength, MappingQualityZeroFraction and TechnologyComposition to Private - VariantType, TransmissionDisequilibriumTest, MVLikelihoodRatio and GCContent are no longer Experimental - AlleleBalanceBySample, HardyWeinberg and HomopolymerRun are Experimental and available to users with a big bold caveat message - Refactored getMeanAltAlleleLength() out of AverageAltAlleleLength into GATKVariantContextUtils in order to make QualByDepth independent of where AverageAltAlleleLength lives - Unrelated change, bundled in for convenience: made HC argument includeUnmappedreads @Hidden - Removed unnecessary check in AverageAltAlleleLength		2013-03-14 14:26:48 -04:00
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java	Cleaned up annotations	2013-03-14 14:26:48 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00