Package org.broadinstitute.gatk.utils.recalibration.covariates

Examples of org.broadinstitute.gatk.utils.recalibration.covariates.RepeatCovariate.initialize()


        Arrays.fill(delQuals, (byte)PairHMMLikelihoodCalculationEngine.INITIAL_QSCORE);

        engine.applyPCRErrorModel(readString.getBytes(), insQuals, delQuals);

        final RepeatCovariate repeatCovariate = new RepeatLengthCovariate();
        repeatCovariate.initialize(PairHMMLikelihoodCalculationEngine.MAX_STR_UNIT_LENGTH, PairHMMLikelihoodCalculationEngine.MAX_REPEAT_LENGTH);

        for ( int i = 1; i < insQuals.length; i++ ) {

            final int repeatLengthFromCovariate = repeatCovariate.findTandemRepeatUnits(readString.getBytes(), i-1).getSecond();
            final byte adjustedScore = PairHMMLikelihoodCalculationEngine.getErrorModelAdjustedQual(repeatLengthFromCovariate, 3.0);
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