Eric Banks 300b474c96 Several improvements to the single sample combining steps. ... 1. updated QualByDepth not to use AD-restricted depth if it is zero. Added unit test this change. 2. Fixed small bug in CombineGVCFs where spanning deletions were not being treated consistently throughout. Added test for this situation. 3. Make sure GenotypeGVCFs puts in the required headers. Updated test files to make sure this is covered. 4. Have GenotypeGVCFs propagate up the MLEAC/AF (which were getting clobbered out). Tests updated to account for this.		2014-02-12 10:15:12 -05:00
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gatk-protected	Several improvements to the single sample combining steps.	2014-02-12 10:15:12 -05:00
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
pom.xml	Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script.	2014-02-03 13:50:46 -05:00