ebanks dc96879861 2 separate changes which both affect lots of UG integration md5s, so I'm committing them together: ... 1. allele balance annotation is now weighted by genotype quality (so we don't get misled by borderline het calls) 2. Updates to the Unified Genotyper for parallelization: a. verbose writing now works again; arg was moved from UAC to UG b. UG checks for command that don't work with parallelization c. some cleanup git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2432 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-23 19:03:56 +00:00
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datasources	Updated, optimized REadBackedPileup. Updated test that was breaking the build -- it created a pileup from reads without bases...	2009-11-25 23:30:39 +00:00
executive	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
io	Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.	2009-09-16 08:33:56 +00:00
iterators	a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads.	2009-11-05 05:26:33 +00:00
refdata	Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same.	2009-12-18 22:54:56 +00:00
traversals	Fix	2009-12-17 17:55:00 +00:00
walkers	2 separate changes which both affect lots of UG integration md5s, so I'm committing them together:	2009-12-23 19:03:56 +00:00
GATKArgumentCollectionTest.java	Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.	2009-09-29 22:23:19 +00:00