ebanks bd2a46ab4c I want to move over to hpprojects tonight, so I'm checking in various changes all in one go: ... 1. Initial code for annotating calls with the base mismatch rate within a reference window (still needs analysis). 2. Move error checking code from rodVCF to VCFRecord. 3. More improvements to SNP Genotype callset concordance. 4. Fixed some comments in Variation/Genotype git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2341 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-13 02:52:18 +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	cleanup of the traversal output code	2009-11-12 06:18:10 +00:00
walkers	I want to move over to hpprojects tonight, so I'm checking in various changes all in one go:	2009-12-13 02:52:18 +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