Replace ACMG_EVIDENCE ',' separator with '&' in VCF (#621)

* fix: use '&' as acmg sep

* test: add mult acmg evidence vcf test

---------

Co-authored-by: Jules Jacobsen <j.jacobsen@qmul.ac.uk>

Author: znorgaard

exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/VcfResultsWriter.java

@@ -249,7 +249,7 @@ private String toVcfAcmgInfo(AcmgEvidence acmgEvidence) {
                     AcmgCriterion.Evidence evidence = entry.getValue();
                     return (acmgCriterion.evidence() == evidence) ? acmgCriterion.toString() : acmgCriterion + "_" + evidence.displayString();
                 })
-                .collect(joining(","));
+                .collect(joining("&"));
     }
 
     private String getRepresentativeAnnotation(List<TranscriptAnnotation> annotations) {

exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/VcfResultsWriterTest.java

@@ -409,6 +409,51 @@ void testAnnotatedVariantAcmgDiseaseNameWhitespaceIsReplacedWithUnderscore() {
     }
 
     @Test
+    public void testMultipleAcmgEvidenceInstancesAreJoinedByAmpersand() {
+        GeneIdentifier geneIdentifier = GeneIdentifier.builder()
+                .geneId("2263")
+                .geneSymbol("FGFR2")
+                .hgncId("HGNC:3689")
+                .hgncSymbol("FGFR2")
+                .entrezId("2263")
+                .ensemblId("ENSG00000066468")
+                .ucscId("uc021pzz.1")
+                .build();
+
+        Gene gene = new Gene(geneIdentifier);
+        VariantEvaluation variant = TestVariantFactory.buildVariant(10, 123256215, "T", "G", SampleGenotype.het(), 30, 2.2);
+        variant.addFilterResult(FilterResult.pass(FilterType.VARIANT_EFFECT_FILTER));
+        variant.addFilterResult(FilterResult.pass(FilterType.INHERITANCE_FILTER));
+        variant.setCompatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT));
+        variant.setContributesToGeneScoreUnderMode(ModeOfInheritance.AUTOSOMAL_DOMINANT);
+        gene.addVariant(variant);
+        gene.addPriorityResult(new OmimPriorityResult(gene.getEntrezGeneID(), gene.getGeneSymbol(), 1f, Collections.emptyList(), Collections.emptyMap()));
+        gene.setCompatibleInheritanceModes(EnumSet.of(ModeOfInheritance.AUTOSOMAL_DOMINANT));
+
+        Disease disease = Disease.builder()
+                .diseaseId("OMIM:101600")
+                .diseaseName("Pfeiffer syndrome")
+                .build();
+
+        GeneScore adScore = GeneScore.builder()
+                .acmgAssignments(List.of(AcmgAssignment.of(variant, geneIdentifier, ModeOfInheritance.AUTOSOMAL_DOMINANT, disease, AcmgEvidence.of(Map.of(
+                        AcmgCriterion.PS3, AcmgCriterion.Evidence.STRONG,
+                        AcmgCriterion.PM2, AcmgCriterion.Evidence.MODERATE,
+                        AcmgCriterion.PP3, AcmgCriterion.Evidence.SUPPORTING
+                )), AcmgClassification.PATHOGENIC)))
+                .contributingVariants(List.of(variant))
+                .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT)
+                .geneIdentifier(geneIdentifier)
+                .combinedScore(1.0)
+                .build();
+        gene.addGeneScore(adScore);
+
+        AnalysisResults analysisResults = buildAnalysisResults(sample, analysis, gene);
+
+        String vcf = instance.writeString(analysisResults, settings);
+        final String expected = METADATA_HEADER + CHR_10_CONTIG_HEADER + SAMPLE_HEADER
+                + "10\t123256215\t.\tT\tG\t2.20\tPASS\tExomiser={1|10-123256215-T-G_AD|FGFR2|2263|AD|1.0000|1.0000|0.0000|0.0000|0.6000|1|0|missense_variant|FGFR2:uc021pzz.1:c.1694A>C:p.(Glu565Ala)|PATHOGENIC|PS3&PM2&PP3|OMIM:101600|\"Pfeiffer_syndrome\"}\tGT:RD\t0/1:30\n";
+        assertThat(vcf, equalTo(expected));
     void nullVcfPathProducesNoOutfile(@TempDir Path tempDir) throws IOException {
         Sample vcfv4Dot3Sample = Sample.builder().vcfPath(null).build();