Examples of iterateInSampleNameOrder()

Examples of htsjdk.variant.variantcontext.GenotypesContext.iterateInSampleNameOrder()

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            return null;

        final ArrayList<Double> refQuals = new ArrayList<Double>();
        final ArrayList<Double> altQuals = new ArrayList<Double>();

        for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) {
            PerReadAlleleLikelihoodMap indelLikelihoodMap = null;
            ReadBackedPileup pileup = null;


            if (stratifiedContexts != null) { // the old UG SNP-only path through the annotations
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Examples of htsjdk.variant.variantcontext.GenotypesContext.iterateInSampleNameOrder()

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            return null;

        final ArrayList<Double> refQuals = new ArrayList<>();
        final ArrayList<Double> altQuals = new ArrayList<>();

        for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) {

            boolean usePileup = true;

            if ( stratifiedPerReadAlleleLikelihoodMap != null ) {
                final PerReadAlleleLikelihoodMap likelihoodMap = stratifiedPerReadAlleleLikelihoodMap.get(genotype.getSampleName());
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