Address comments

broadinstitute · Oct 23, 2019 · c5b0ba6 · c5b0ba6
1 parent 712a331
commit c5b0ba6
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Showing 2 changed files with 10 additions and 14 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoods.java b/src/main/java/org/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoods.java
@@ -352,10 +352,10 @@ public void normalizeLikelihoods(final double maximumLikelihoodDifferenceCap) {
     private void normalizeLikelihoodsPerEvidence(final double maximumBestAltLikelihoodDifference,
                                                  final double[][] sampleValues, final int sampleIndex, final int evidenceIndex) {
 
-        //allow the best "alternative" allele to be the reference because asymmetry leads to strange artifacts like het calls with >90% alt reads
-        final BestAllele bestAlternativeAllele = searchBestAllele(sampleIndex,evidenceIndex,true);
+        //allow the best allele to be the reference because asymmetry leads to strange artifacts like het calls with >90% alt reads
+        final BestAllele bestAllele = searchBestAllele(sampleIndex,evidenceIndex,true);
 
-        final double worstLikelihoodCap = bestAlternativeAllele.likelihood + maximumBestAltLikelihoodDifference;
+        final double worstLikelihoodCap = bestAllele.likelihood + maximumBestAltLikelihoodDifference;
 
         final int alleleCount = alleles.numberOfAlleles();
 

diff --git a/...oadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/...oadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -1228,18 +1228,14 @@ public void testContaminatedHomVarDeletions() {
 
         final File outputContaminatedHomVarDeletions = createTempFile("testContaminatedHomVarDeletions", ".vcf");
 
-        // Run both with and without --max-alternate-alleles over our interval, so that we can
-        // prove that the argument is working as intended.
-        final String[] argsNoMaxAlternateAlleles = {
-                "-I", bam,
-                "-R", hg38Reference,
-                "-L", intervals,
-                "-O", outputContaminatedHomVarDeletions.getAbsolutePath(),
-                "--interval-padding", "50"
-        };
-        runCommandLine(argsNoMaxAlternateAlleles);
+        final ArgumentsBuilder args = new ArgumentsBuilder().addInput(new File(bam))
+                .addReference(hg38Reference)
+                .addInterval(new SimpleInterval(intervals))
+                .addOutput(outputContaminatedHomVarDeletions)
+                .addNumericArgument(IntervalArgumentCollection.INTERVAL_PADDING_LONG_NAME, 50);
+        runCommandLine(args);
 
-        List<VariantContext> vcs = VariantContextTestUtils.readEntireVCFIntoMemory(outputContaminatedHomVarDeletions.getAbsolutePath()).getRight();
+        List<VariantContext> vcs = VariantContextTestUtils.getVariantContexts(outputContaminatedHomVarDeletions);
 
         //check known homozygous deletion for correct genotype
         for (final VariantContext vc : vcs) {