Fix for issue #481 where TSV and VCF results files would contain no d…

…ata when the analysis `inheritanceModes` was empty.

exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/Gene.java

@@ -359,12 +359,22 @@ public List<GeneScore> getGeneScores() {
      * @return A list of {@link GeneScore} with a compatible mode of inheritance.
      */
     public List<GeneScore> getCompatibleGeneScores() {
-        return this.geneScoreMap.entrySet().stream()
-                .filter(entry -> this.inheritanceModes.contains(entry.getKey()))
+        // An explanation about the logic here: If the Analysis.inheritanceModes is empty or no MOI dependent analysis
+        // step has been run the (compatible) inheritanceModes will be empty. The GeneScorer will always give a gene a
+        // GeneScore but in this case it will have an MOI.ANY. So, in the case that no compatible inheritanceModes are
+        // present, the ANY GeneScore should be returned here otherwise the ResultsWriters relying on this method
+        // (TSV and VCF) will return empty data. See issue https://github.com/exomiser/Exomiser/issues/481
+        return inheritanceModes.isEmpty() ? anyMoiScoreOrEmptyList() : geneScoreMap.entrySet().stream()
+                .filter(entry -> inheritanceModes.contains(entry.getKey()))
                 .map(Map.Entry::getValue)
                 .collect(Collectors.toUnmodifiableList());
     }
 
+    private List<GeneScore> anyMoiScoreOrEmptyList() {
+        GeneScore geneScore = geneScoreMap.get(ModeOfInheritance.ANY);
+        return geneScore != null ? List.of(geneScore) : List.of();
+    }
+
     public GeneScore getGeneScoreForMode(ModeOfInheritance modeOfInheritance) {
         Objects.requireNonNull(modeOfInheritance);
         return geneScoreMap.getOrDefault(modeOfInheritance, GeneScore.builder()

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

@@ -20,21 +20,17 @@
 
 package org.monarchinitiative.exomiser.core.writers;
 
-import de.charite.compbio.jannovar.mendel.ModeOfInheritance;
 import org.monarchinitiative.exomiser.api.v1.OutputProto;
-import org.monarchinitiative.exomiser.core.analysis.Analysis;
 import org.monarchinitiative.exomiser.core.analysis.AnalysisResults;
-import org.monarchinitiative.exomiser.core.analysis.util.InheritanceModeOptions;
-import org.monarchinitiative.exomiser.core.model.Gene;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.Collections;
 import java.util.EnumSet;
 import java.util.Set;
-import java.util.Collections;
 
 /**
  * Facade for handling writing out {@link org.monarchinitiative.exomiser.core.analysis.AnalysisResults}

exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/GeneTest.java

@@ -758,8 +758,31 @@ public void testGetCompatibleGeneScores() throws Exception {
                 .addMixIn(Variant.class, JsonVariantMixin.class)
                 .setDefaultPropertyInclusion(JsonInclude.Include.NON_DEFAULT)
                 .writerWithDefaultPrettyPrinter();
-        System.out.println(objectWriter.writeValueAsString(instance));
 
+        assertThat(instance.getCompatibleInheritanceModes(), equalTo(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)));
         assertThat(instance.getCompatibleGeneScores(), equalTo(List.of(adGeneScore)));
     }
+
+    @Test
+    public void testGetCompatibleGeneScoresNoCompatibleMoi() throws Exception {
+        Gene instance = TestFactory.newGeneFGFR2();
+        // Hmm... this is a bit of a WFT - why does this need to be set rather than computed from the variants?
+        //  ... because it gets set once by the InheritanceModeAnalyser after all the variants have been filtered
+//        instance.setCompatibleInheritanceModes(EnumSet.of(ModeOfInheritance.AUTOSOMAL_DOMINANT));
+        assertThat(instance.getCompatibleGeneScores().isEmpty(), is(true));
+
+        GeneScore anyGeneScore = GeneScore.builder()
+                .geneIdentifier(instance.getGeneIdentifier())
+                .modeOfInheritance(ModeOfInheritance.ANY)
+                .phenotypeScore(0.5d)
+                .variantScore(0.5d)
+                .combinedScore(0.5d)
+                .pValue(0.0000001)
+                .build();
+
+        instance.addGeneScore(anyGeneScore);
+
+        assertThat(instance.getCompatibleInheritanceModes().isEmpty(), is(true));
+        assertThat(instance.getCompatibleGeneScores(), equalTo(List.of(anyGeneScore)));
+    }
 }