Examples of org.broad.igv.variant.Genotype

            genotypeMap.put(sample, vcfGenotype);
        }


        zygosityCount = new ZygosityCount();
        for (String sample : getSampleNames()) {
            Genotype genotype = getGenotype(sample);
            zygosityCount.incrementCount(genotype);
        }


        String afString = null;
        String[] alleleFreqKeys = {"AF", "GMAF"};

        double methTotal = 0;
        int samplesWithData = 0;
        final int size = getSampleNames().size();
        if (size > 0) {
            for (String sample : getSampleNames()) {
                Genotype genotype = getGenotype(sample);
                double mr = genotype.getAttributeAsDouble("MR");
                double goodBaseCount = genotype.getAttributeAsDouble("MR");
                if (!Double.isNaN(mr) && !Double.isNaN(goodBaseCount) && goodBaseCount > VariantTrack.METHYLATION_MIN_BASE_COUNT) {
                    methTotal += mr;
                    samplesWithData++;
                }
            }

Related Classes of org.broad.igv.variant.Genotype

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