Mark DePristo dcc972a557 Usability cleanup for BQSR ... -- I'm seeing a lot of people trying to use BinaryTagCovariate in the community. They really shouldn't do this, so I moved it to private. -- Throw an exception if its required bintag argument is missing -- Check explicitly if user is requesting DinucCovariate and tell them that its been retired in favor of ContextCovariate -- Show the type (Required, Experimental, Standard) of the covariates when running --list		2012-08-25 14:53:00 -04:00
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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	Usability cleanup for BQSR	2012-08-25 14:53:00 -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