Eric Banks f657b8bda8 Complete overhaul of the BQSRv2 integration tests. Much more comprehensive. Still need to deal with a few tests that need some modifications before I'm done, but I'll take care of that sometime tomorrow.		2012-07-17 00:32:34 -04:00
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src/org/broadinstitute/sting	Add utility decorators so that classes can tell you which package source they come from if they want to (suggested by Khalid). Using those decorators, we can easily pull out the BQSR updateDataForPileupElement() method into a standard RecalibrationEngine and an AdvancedRecalibrationEngine and use the protected one (AdvancedRE) if available (otherwise, the public one).	2012-07-16 15:34:50 -04:00
test/org/broadinstitute/sting/gatk/walkers	Complete overhaul of the BQSRv2 integration tests. Much more comprehensive. Still need to deal with a few tests that need some modifications before I'm done, but I'll take care of that sometime tomorrow.	2012-07-17 00:32:34 -04:00