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chartl 90212c643b more effective & efficient test for SecondBaseSkew 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2075 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-11-18 20:53:32 +00:00
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datasources Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests. 2009-09-30 20:37:59 +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 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated. 2009-11-16 02:41:20 +00:00
traversals cleanup of the traversal output code 2009-11-12 06:18:10 +00:00
walkers more effective & efficient test for SecondBaseSkew 2009-11-18 20:53:32 +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