weird bug in dynamic read disqualification fixed

broadinstitute · Dec 10, 2022 · 12d8623 · 12d8623
1 parent 894117c
commit 12d8623
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/...nstitute/hellbender/tools/walkers/haplotypecaller/FlowBasedAlignmentLikelihoodEngine.java b/...nstitute/hellbender/tools/walkers/haplotypecaller/FlowBasedAlignmentLikelihoodEngine.java
@@ -109,12 +109,12 @@ public AlleleLikelihoods<GATKRead, Haplotype> computeReadLikelihoods(final List<
     @Override
     public ToDoubleFunction<GATKRead> log10MinTrueLikelihood(final double expectedErrorRate, final boolean capLikelihoods) {
         final double log10ErrorRate = Math.log10(expectedErrorRate);
-        final double catastrophicErrorRate = Math.log10(fbargs.fillingValue);
-
+        final double catastrophicErrorRate = fbargs.fillingValue;
+        final double log10catastrophicErrorRate = Math.log10(fbargs.fillingValue);
         return read -> {
             final double maxErrorsForRead = capLikelihoods ? Math.max(MAX_ERRORS_FOR_READ_CAP, Math.ceil(read.getLength() * expectedErrorRate)) : Math.ceil(read.getLength() * expectedErrorRate);
             final double maxCatastrophicErrorsForRead = capLikelihoods ? Math.max(MAX_CATASTROPHIC_ERRORS_FOR_READ_CAP, Math.ceil(read.getLength() * catastrophicErrorRate)) : Math.ceil(read.getLength() * catastrophicErrorRate);
-            return maxErrorsForRead * log10ErrorRate + maxCatastrophicErrorsForRead * catastrophicErrorRate;
+            return maxErrorsForRead * log10ErrorRate + maxCatastrophicErrorsForRead * log10catastrophicErrorRate;
         };
     }