@Test
public void testHomozygousAltAlleleOutputVcfContainsConcatenatedVariantScoresOnOneLine() {

    Path vcfPath = Paths.get("src/test/resources/multiAlleleGenotypes.vcf");
    VariantFactory variantFactory = TestFactory.buildDefaultVariantFactory();
    List<VariantEvaluation> variants = variantFactory.createVariantEvaluations(vcfPath).collect(toList());
    variants.forEach(System.out::println);
    // 1/2 HETEROZYGOUS_ALT - needs to be written back out as a single line
    VariantEvaluation altAlleleOne = variants.get(3);
    //change the variant effect from MISSENSE so that the score is different and the order can be tested on the output line
    //variant score is 0.95 - contributes to score
    altAlleleOne.setVariantEffect(VariantEffect.FRAMESHIFT_VARIANT);
    altAlleleOne.setContributesToGeneScoreUnderMode(ModeOfInheritance.AUTOSOMAL_DOMINANT);
    //variant score is 0.6
    VariantEvaluation altAlleleTwo = variants.get(4);
    Gene gene = new Gene(GeneIdentifier.builder()
            .geneSymbol(altAlleleOne.getGeneSymbol())
            .geneId(altAlleleOne.getGeneId())
            .build());
    gene.addVariant(altAlleleOne);
    gene.addVariant(altAlleleTwo);
    gene.setCompatibleInheritanceModes(EnumSet.of(ModeOfInheritance.AUTOSOMAL_DOMINANT));
    AnalysisResults analysisResults = buildAnalysisResults(gene);
    String output = instance.writeString(ModeOfInheritance.AUTOSOMAL_DOMINANT, analysis, analysisResults, settings);
    System.out.println(output);
    //expected should have concatenated variant score for multi-allele line: ExVarSCombi=0.85,0.6
    String expected = EXPECTED_HEADER
            + "10\t123256215\t.\tT\tG,A\t100\t.\tExContribAltAllele=0;ExGeneSCombi=0.0;ExGeneSPheno=0.0;ExGeneSVar=0.0;ExGeneSymbId=2263;ExGeneSymbol=FGFR2;ExVarEff=frameshift_variant,missense_variant;ExVarHgvs=10:g.123256215T>G,10:g.123256215T>A;ExVarScore=1.0,0.6;GENE=FGFR2;INHERITANCE=AD;MIM=101600\tGT\t1/2\n";
    assertThat(output, equalTo(expected));
}