Fix a few straggling issues from multiple raw keys`

broadinstitute · Sep 18, 2019 · 9dd22f2 · 9dd22f2
1 parent 332c40f
commit 9dd22f2
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepthUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepthUnitTest.java
@@ -224,7 +224,8 @@ public void testAnnotate_AS() throws Exception {
     @Test
     public void testDescriptions_AS() throws Exception {
         final AS_QualByDepth cov = new AS_QualByDepth();
-        Assert.assertEquals(cov.getRawKeyNames(), GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY);
+        Assert.assertEquals(cov.getRawKeyNames().get(0), GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY);
+        Assert.assertEquals(cov.getRawKeyNames().get(1), GATKVCFConstants.AS_QUAL_KEY);
         Assert.assertEquals(cov.getDescriptions().size(), 1);
         Assert.assertEquals(cov.getDescriptions().get(0).getID(), GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY);
     }

diff --git a/...java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java b/...java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java
@@ -40,7 +40,7 @@ public void testDescriptions() throws Exception {
         Assert.assertEquals(cov.getDescriptions().get(0).getID(), VCFConstants.RMS_MAPPING_QUALITY_KEY);
         Assert.assertEquals(cov.getRawDescriptions().size(), 1);
         Assert.assertEquals(cov.getRawDescriptions().get(0).getID(), GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY);
-        Assert.assertEquals(new RMSMappingQuality().getRawKeyNames(), GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY);
+        Assert.assertEquals(new RMSMappingQuality().getRawKeyNames().get(0), GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY);
         Assert.assertEquals(new RMSMappingQuality().getKeyNames(), Sets.newHashSet(VCFConstants.RMS_MAPPING_QUALITY_KEY, GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY));
     }
 
@@ -201,7 +201,7 @@ public void testCombineAndFinalize() {
         final RMSMappingQuality annotator = RMSMappingQuality.getInstance();
 
         final Map<String, Object> combined = annotator.combineRawData(vcAlleles, combinedVCdata);
-        final String combinedListString = (String)combined.get(annotator.getRawKeyNames());
+        final String combinedListString = (String)combined.get(annotator.getRawKeyNames().get(0));
         Assert.assertEquals(combinedListString, "69640,20");
 
         final VariantContext vc = new VariantContextBuilder(makeVC())
@@ -224,7 +224,7 @@ public void testCombineAndFinalizeHighMQSquared() {
         final RMSMappingQuality annotator = RMSMappingQuality.getInstance();
 
         final Map<String, Object> combined = annotator.combineRawData(vcAlleles, combinedVCdata);
-        final String combinedListString = (String)combined.get(annotator.getRawKeyNames());
+        final String combinedListString = (String)combined.get(annotator.getRawKeyNames().get(0));
         Assert.assertEquals(combinedListString, "11925002601,5500001");
 
         final VariantContext vc = new VariantContextBuilder(makeVC())