Eric Banks 6bee6a1b53 Change the behavior of SelectVariants for PL/AD when it encounters a record that has lost one or more alternate alleles. ... Previously, we would strip out the PLs and AD values since they were no longer accurate. However, this is not ideal because then that information is just lost and 1) users complain on the forum and post it as a bug and 2) it gives us problems in both the current and future (single sample) calling pipelines because we subset samples/alleles all the time and lose info. Now the PLs and AD get correctly selected down. While I was in there I also refactored some related code in subsetDiploidAlleles(). There were no real changes there - I just broke it out into smaller chunks as per our best practices. Added unit tests and updated integration tests. Addressed reviews.		2013-12-03 09:23:03 -05:00
..
java	Change the behavior of SelectVariants for PL/AD when it encounters a record that has lost one or more alternate alleles.	2013-12-03 09:23:03 -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