Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.GenotypeType

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            if (f != null) {
                String selectedSample = getSampleAtPosition(te.getMouseEvent().getY());
                if (selectedSample != null) {
                    // Select clicked sample and all other adjacent with the same genotype
                    Genotype genotype = f.getGenotype(selectedSample);
                    GenotypeType type = genotype.getType();

                    int idx = getSampleIndex(selectedSample);
                    for (int i = idx; i < sampleBounds.size(); i++) {
                        String s = sampleBounds.get(i).sample;
                        Genotype gt = f.getGenotype(s);
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        boolean isComplexEvent = isComplexEventCB.isSelected();

        int allele0 = -1;
        int allele1 = -1;

        GenotypeType gtt = (GenotypeType) genotypeTypeField.getSelectedItem();
        switch (gtt) {
            case HOM_REF:
                allele0 = allele1 = 0;
                break;
            case HOM_VAR:
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    }

    private void initGenotypeTypeField(VariantContext variant) {
        String mutationString = null;
        GenotypeType gtt = GenotypeType.NO_CALL;
        String prefSampleName = VariantReviewPlugin.getPreferentialSampleName();

        //If there is only one sample, or we find the preferential sample,
        //use that data.
        for (String sampleName : variant.getSampleNamesOrderedByName()) {
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Related Classes of htsjdk.variant.variantcontext.GenotypeType

  • org.broad.igv.plugin.mongovariant.VariantReviewDialog
  • org.broad.igv.variant.VariantTrack
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