Mark DePristo 74196ff7db Trivial BQSR bug fixes and improvement ... -- Ensure that BQSR works properly for an Ion Torrent BAM. (Added integration test and bam) -- Improve the error message when a unknown platform is found (integration test added)		2013-04-11 17:08:35 -04:00
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covariates	Trivial BQSR bug fixes and improvement	2013-04-11 17:08:35 -04:00
BQSRReadTransformer.java	Added the functionality to impose a relative ordering on ReadTransformers in the GATK engine.	2013-03-06 12:38:59 -05:00
BaseRecalibration.java	Cleanup and unit tests for QualityUtils	2013-02-16 07:31:37 -08:00
QualQuantizer.java	Cleanup and unit tests for QualityUtils	2013-02-16 07:31:37 -08:00
QuantizationInfo.java	Cleanup and unit tests for QualityUtils	2013-02-16 07:31:37 -08:00
ReadCovariates.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
RecalDatum.java	Cleanup and unit tests for QualityUtils	2013-02-16 07:31:37 -08:00
RecalDatumNode.java	Move some VCF/VariantContext methods back to the GATK based on feedback	2013-01-29 16:56:55 -05:00
RecalUtils.java	Made some documentation updates & fixes	2013-03-20 06:15:20 -04:00
RecalibrationReport.java	Updating BQSR RecalibrationEngine to work correctly with empty BQSR tables.	2013-04-11 16:27:59 -04:00
RecalibrationTables.java	Updating BQSR RecalibrationEngine to work correctly with empty BQSR tables.	2013-04-11 16:27:59 -04:00