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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/recalibration
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Mark DePristo 7bf1f67273 BQSR optimization: read group x quality score calibration table is thread-local 
-- AdvancedRecalibrationEngine now uses a thread-local table for the quality score table, and in finalizeData merges these thread-local tables into the final table.  Radically reduces the contention for RecalDatum in this very highly used table
-- Refactored the utility function to combine two tables into RecalUtils, and created UnitTests for this function, as well as all of RecalibrationTables.  Updated combine in RecalibrationReport to use this table combiner function
-- Made several core functions in RecalDatum into final methods for performance
-- Added RecalibrationTestUtils, a home for recalibration testing utilities
 		2012-12-24 13:35:58 -05:00
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ContextCovariateUnitTest.java Cleanup BQSR classes 2012-07-31 08:11:03 -04:00
CycleCovariateUnitTest.java The user can now set the maximum allowable cycle on the command-line with --maximum_cycle_value. This value is (now) enforced in the Cycle covariate and a User Error is thrown if the maximum value is passed (with a helpful error message). Added unit tests to cover this new functionality. 2012-11-20 22:41:57 -05:00
QualQuantizerUnitTest.java Ready for full-scale evaluation adaptive BQSR contexts 2012-08-03 16:02:53 -04:00
ReadCovariatesUnitTest.java Cleanup BQSR classes 2012-07-31 08:11:03 -04:00
ReadGroupCovariateUnitTest.java Cleanup BQSR classes 2012-07-31 08:11:03 -04:00
RecalDatumUnitTest.java RecalDatums now hold doubles so the test for equality needs an epsilon. 2012-08-28 16:00:52 -04:00
RecalUtilsUnitTest.java BQSR optimization: read group x quality score calibration table is thread-local 2012-12-24 13:35:58 -05:00
RecalibrationReportUnitTest.java Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table. 2012-09-20 14:14:34 -04:00
RecalibrationTablesUnitTest.java BQSR optimization: read group x quality score calibration table is thread-local 2012-12-24 13:35:58 -05:00
RecalibrationTestUtils.java BQSR optimization: read group x quality score calibration table is thread-local 2012-12-24 13:35:58 -05:00