Mark DePristo e00ed8bc5e Cleanup BQSR classes ... -- Moved most of BQSR classes (which are used throughout the codebase) to utils.recalibration. It's better in my opinion to keep commonly used code in utils, and only specialized code in walkers. As code becomes embedded throughout GATK its should be refactored to live in utils -- Removed unncessary imports of BQSR in VQSR v3 -- Now ready to refactor QualQuantizer and unit test into a subclass of RecalDatum, refactor unit tests into RecalDatum unit tests, and generalize into hierarchical recal datum that can be used in QualQuantizer and the analysis of adaptive context covariate -- Update PluginManager to sort the plugins and interfaces. This allows us to have a deterministic order in which the plugin classes come back, which caused BQSR integration tests to temporarily change because I moved my classes around a bit.		2012-07-31 08:11:03 -04:00
..
GATKLiteUtils.java	Register GATK-full-only walkers and rethrow the missing walker error as a not supported in GATK lite error	2012-07-25 14:11:03 -04:00
JVMUtils.java	As requested by Mark, I've broken out the code to pull out the protected subclass when available (and otherwise use the public version) into the GATKLiteUtils class. People should use this code instead of reimplementing all of the java reflection on their own.	2012-07-18 22:44:37 -04:00
PluginManager.java	Cleanup BQSR classes	2012-07-31 08:11:03 -04:00
ProtectedPackageSource.java	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
PublicPackageSource.java	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