hanna 2bd0b1bbf7 After further review, it's unclear that my patch in RecalDataManager was the right choice. Reverting. ... Also updating other IntervalCleanerIntegrationTest failures that were masked by my first patch. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2440 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-24 00:32:33 +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	After further review, it's unclear that my patch in RecalDataManager was the right choice. Reverting.	2009-12-24 00:32:33 +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