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Searched refs:calculateSOR (Results 1 – 5 of 5) sorted by relevance

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/
H A DStrandOddsRatio.java129 …return tableFromPerSampleAnnotations != null ? annotationForOneTable(calculateSOR(tableFromPerSamp… in calculateAnnotationFromGTfield()
136 return annotationForOneTable(calculateSOR(table)); in calculateAnnotationFromLikelihoods()
149 public static double calculateSOR(final int[][] table) { in calculateSOR() method in StrandOddsRatio
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/
H A DAS_StrandOddsRatio.java90 final double ratio = StrandOddsRatio.calculateSOR(table); in calculateAnnotationFromLikelihoods()
103 annotationMap.put(a,StrandOddsRatio.calculateSOR(refAltTable)); in calculateReducedData()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/
H A DStrandOddsRatioUnitTest.java61 final double ratio = StrandOddsRatio.calculateSOR(contingencyTable); in testUsingSOR()
92 final double expectedSOR = StrandOddsRatio.calculateSOR(new int[][]{{1,2},{3,4}}); in testUsingGT()
131 final double expectedSOR = StrandOddsRatio.calculateSOR(table); in testUsingLikelihoods()
H A DVariantAnnotatorEngineUnitTest.java188 …TRAND_ODDS_RATIO_KEY), StrandOddsRatio.formattedValue(StrandOddsRatio.calculateSOR(new int[][]{{re… in testAllAnnotations()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/
H A DGnarlyGenotyperEngine.java238 …STRAND_ODDS_RATIO_KEY, StrandOddsRatio.formattedValue(StrandOddsRatio.calculateSOR(StrandBiasTest.… in finalizeGenotype()