Examples of FastLoglessPairHMM

    }


    @SuppressWarnings("unused")
    public void timeGraphBasedLikelihoods(final int reps) {
        for (int i = 0; i < reps; i++) {
            final GraphBasedLikelihoodCalculationEngineInstance rtlce = new GraphBasedLikelihoodCalculationEngineInstance(dataSet.assemblyResultSet(), new FastLoglessPairHMM((byte)10),Double.NEGATIVE_INFINITY,HeterogeneousKmerSizeResolution.COMBO_MAX);
            rtlce.computeReadLikelihoods(dataSet.haplotypeList(), SampleListUtils.singletonList("anonymous"), Collections.singletonMap("anonymous", dataSet.readList()));
        }
    }

Examples of org.broadinstitute.gatk.utils.pairhmm.FastLoglessPairHMM

     */
    public GraphBasedLikelihoodCalculationEngine(final int gapExtensionPenalty, final double log10GlobalReadMismappingRate,
                                                 final HeterogeneousKmerSizeResolution heterogeneousKmerSizeResolution,
                                                 final boolean debug, final boolean debugHaplotypeGraphAndLikelihoods) {
        gcpHMM = (byte) gapExtensionPenalty;
        hmm = new FastLoglessPairHMM(gcpHMM);
        this.log10GlobalReadMismappingRate = log10GlobalReadMismappingRate;
        this.heterogeneousKmerSizeResolution = heterogeneousKmerSizeResolution;
        debugMode = debugHaplotypeGraphAndLikelihoods ? DebugMode.EXTRA_DEBUG : debug ? DebugMode.DEBUG : DebugMode.NONE;
    }

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