chartl 23983b2fd8 New annotation: ResidualQuality ... Computes a metric for how much error is left that isn't explained by ref or snp bases. This is the sum of Q scores, weighted by the proportion of non-ref non-snp bases to non-snp bases. Reported in Log space. Update to the integration test so bamboo doesn't look as though someone murdered it with a spork git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2124 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-23 20:04:01 +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	Fixed the sample mix-up bug Kiran discovered, and added a unit test in the VCF reader class (Thanks for the good example files Kiran). Also renamed the toStringRepresentation function to toStringEncoding, and added a matching method in VCFGenotypeRecord.	2009-11-19 18:17:47 +00:00
traversals	cleanup of the traversal output code	2009-11-12 06:18:10 +00:00
walkers	New annotation: ResidualQuality	2009-11-23 20:04:01 +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