Introduce output of hets on overlapping reads

PankratzLab · Jan 25, 2019 · ff79852 · ff79852
1 parent 753c201
commit ff79852
Showing 1 changed file with 13 additions and 1 deletion.
diff --git a/supernovo/src/main/java/org/pankratzlab/supernovo/output/DeNovoResult.java b/supernovo/src/main/java/org/pankratzlab/supernovo/output/DeNovoResult.java
@@ -109,6 +109,9 @@ public Pileup getPileup() {
   public final boolean deNovo;
   public final boolean superNovo;
   public final double meanHaplotypeConcordance;
+  public final int overlappingReadsHetCount;
+  public static final double MIN_HAPLOTYPE_CONCORDANCE = 0.95;
+  public final int overlappingReadsDiscordantHetCount;
   public final int overlappingReadsDeNovoCount;
   public final int overlapingReadsThirdAlleleCount;
   public final Sample child;
@@ -149,11 +152,20 @@ public DeNovoResult(
               .mapToDouble(Double::valueOf)
               .summaryStatistics()
               .getAverage();
+    overlappingReadsHetCount = hapResults.getConcordances().size();
+    overlappingReadsDiscordantHetCount =
+        (int)
+            hapResults
+                .getConcordances()
+                .stream()
+                .mapToDouble(Double::valueOf)
+                .filter(d -> d < MIN_HAPLOTYPE_CONCORDANCE)
+                .count();
     superNovo =
         biallelicHeterozygote
             && deNovo
             && hapResults.getOtherDeNovos() == 0
-            && meanHaplotypeConcordance >= 0.95
+            && meanHaplotypeConcordance >= MIN_HAPLOTYPE_CONCORDANCE
             && hapResults.getOtherTriallelics() == 0;
     overlappingReadsDeNovoCount = hapResults.getOtherDeNovos();
     overlapingReadsThirdAlleleCount = hapResults.getOtherTriallelics();