Eric Banks 0a89adbcdb 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
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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	Move BQSRv2 into public and v1 into the archive.	2012-07-16 14:23:38 -04:00