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gatk-3.8/protected/java/src/org/broadinstitute/sting/utils/recalibration
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Ryan Poplin ac033ce41a Intermediate commit of new bubble assembly graph traversal algorithm for the HaplotypeCaller. Adding functionality for a path from an assembly graph to calculate its own cigar string from each of the bubbles instead of doing a massive Smith-Waterman alignment between the path's full base composition and the reference. 2013-01-31 11:32:19 -05:00
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covariates Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
BQSRReadTransformer.java The Bayesian calculation of Qemp in the BQSR is now hierarchical. This fixes issues in which the covariate bins were very sparse and the prior estimate being used was the original quality score. This resulted in large correction factors for each covariate which breaks the equation. There is also now a new option, qlobalQScorePrior, which can be used to ignore the given (very high) quality scores and instead use this value as the prior. 2013-01-28 15:56:33 -05:00
BaseRecalibration.java Adding unit tests for hierarchicalBayesianQualityEstimate function 2013-01-30 13:26:07 -05:00
QualQuantizer.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
QuantizationInfo.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ReadCovariates.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
RecalDatum.java Intermediate commit of new bubble assembly graph traversal algorithm for the HaplotypeCaller. Adding functionality for a path from an assembly graph to calculate its own cigar string from each of the bubbles instead of doing a massive Smith-Waterman alignment between the path's full base composition and the reference. 2013-01-31 11:32:19 -05:00
RecalDatumNode.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
RecalUtils.java Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
RecalibrationReport.java The Empirical quality column in the recalibration report can't be compared in the BQSRGatherer because the value is calculated using the Bayesian estimate with different priors. This value should never be used from a recalibration report anyway except during plotting. 2013-01-30 12:28:14 -05:00
RecalibrationTables.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00