Adding a little more to the integration test to make sure that MAF ou…

…tputs have a header that includes custom fields.
broadinstitute · Jun 22, 2018 · d4a9471 · d4a9471
1 parent 1c866e1
commit d4a9471
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/...org/broadinstitute/hellbender/tools/funcotator/mafOutput/CustomMafFuncotationCreator.java b/...org/broadinstitute/hellbender/tools/funcotator/mafOutput/CustomMafFuncotationCreator.java
@@ -27,7 +27,7 @@
  */
 public class CustomMafFuncotationCreator {
 
-    final static List<String> COUNT_FIELD_NAMES = Arrays.asList(
+    final public static List<String> COUNT_FIELD_NAMES = Arrays.asList(
             MafOutputRendererConstants.FieldName_t_alt_count,
             MafOutputRendererConstants.FieldName_t_ref_count,
             MafOutputRendererConstants.FieldName_n_alt_count,

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java
@@ -14,6 +14,7 @@
 import org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection;
 import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation;
 import org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory;
+import org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator;
 import org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer;
 import org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants;
 import org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer;
@@ -1003,7 +1004,10 @@ public void testNoVariantsProduceMaf() {
 
         final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(outputFile.toPath(), null);
         Assert.assertEquals(maf.getRecords().size(),  0);
-        // TODO: Check for the custom Maf fields
+
+        // Double-check that the custom MAF fields are present.
+        Assert.assertTrue(CustomMafFuncotationCreator.COUNT_FIELD_NAMES.stream()
+                .allMatch(f -> maf.getAnnotations().contains(f)));
     }
 }