ebanks 94f5edb68a 1. Fixed VCFGenotypeRecord bug (it needs to emit fields in the order specified by the GenotypeFormatString) ... 2. isNoCall() added to Genotype interface so that we can distinguish between ref and no calls (all we had before was isVariant()) 3. Added Hardy-Weinberg annotation; still experimental - not working yet so don't use it. 4. Move 'output type' argument out of the UnifiedArgumentCollection and into the UnifiedGenotyper, in preparation for parallelization. 5. Improved some of the UG integration tests. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2398 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-18 04:14:14 +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	Stage 3 of Variation refactoring:	2009-12-08 21:43:28 +00:00
traversals	Fix	2009-12-17 17:55:00 +00:00
walkers	1. Fixed VCFGenotypeRecord bug (it needs to emit fields in the order specified by the GenotypeFormatString)	2009-12-18 04:14:14 +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