Ensure VariantContexts are sorted in ExtendedMultiVariantWalkerGroupe…

…dOnStart, and bugfix to MendelianViolation code when child has one allele (#336)
BimberLab · Jul 25, 2024 · f002b29 · f002b29
1 parent 38a1a58
commit f002b29
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Showing 2 changed files with 11 additions and 1 deletion.
diff --git a/src/main/java/com/github/discvrseq/walkers/ExtendedMultiVariantWalkerGroupedOnStart.java b/src/main/java/com/github/discvrseq/walkers/ExtendedMultiVariantWalkerGroupedOnStart.java
@@ -1,6 +1,7 @@
 package com.github.discvrseq.walkers;
 
 import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.variantcontext.VariantContextComparator;
 import org.broadinstitute.hellbender.engine.FeatureInput;
 import org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart;
 
@@ -34,6 +35,9 @@ protected Map<FeatureInput<VariantContext>, List<VariantContext>> groupVariantsB
             if (!byFeatureInput.containsKey(fi)) {
                 byFeatureInput.put(fi, Collections.emptyList());
             }
+            else {
+                byFeatureInput.get(fi).sort(new VariantContextComparator(getBestAvailableSequenceDictionary()));
+            }
         }
 
         return byFeatureInput;

diff --git a/src/main/java/com/github/discvrseq/walkers/annotator/MendelianViolationCount.java b/src/main/java/com/github/discvrseq/walkers/annotator/MendelianViolationCount.java
@@ -19,6 +19,7 @@
 import org.broadinstitute.hellbender.utils.samples.Sex;
 
 import javax.annotation.Nullable;
+import java.io.Serial;
 import java.util.*;
 
 /**
@@ -161,6 +162,10 @@ public boolean isViolation(){
     }
 
     private static boolean testParents(Genotype gChild, Genotype gDad, Genotype gMom){
+        if (gChild.getAlleles().size() != 2) {
+            return false;
+        }
+
         return !(gMom.getAlleles().contains(gChild.getAlleles().get(0)) && gDad.getAlleles().contains(gChild.getAlleles().get(1)) || gMom.getAlleles().contains(gChild.getAlleles().get(1)) && gDad.getAlleles().contains(gChild.getAlleles().get(0)));
     }
 
@@ -182,10 +187,11 @@ public List<VCFCompoundHeaderLine> getDescriptions() { return Arrays.asList(
     }
 
     public static class NoCallGenotype extends Genotype {
+        @Serial
         private static final long serialVersionUID = 1L;
 
         private Genotype _orig = null;
-        private List<Allele> _alleles = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
+        private final List<Allele> _alleles = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
 
         public NoCallGenotype(String sampleName)
         {