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gatk-3.8/public/java/test/org/broadinstitute/sting
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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
..
commandline Fixed the logic of the @Output annotation and its interaction with 'required'. 2013-03-14 11:58:51 -04:00
gatk Adaptations to accomodate Tribble API changes, comprising mostly of the following. 2013-08-19 15:52:47 -04:00
jna Fix pipeline tests that were not respecting the pipeline test dry run setting 2013-06-28 15:27:17 -04:00
utils 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
BaseTest.java Adding Graph-based likelihood ratio calculation to HC 2013-12-02 19:37:19 -05:00
ExampleToCopyUnitTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00
MD5DB.java Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00
MD5Mismatch.java Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00
StingTextReporter.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java Adding Graph-based likelihood ratio calculation to HC 2013-12-02 19:37:19 -05:00
WalkerTest.java Adding Graph-based likelihood ratio calculation to HC 2013-12-02 19:37:19 -05:00