Addressed PR comment

broadinstitute · Jun 8, 2018 · 30f7ad3 · 30f7ad3
1 parent 76178df
commit 30f7ad3
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Showing 2 changed files with 42 additions and 1 deletion.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotationMap.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotationMap.java
@@ -31,7 +31,6 @@ public class FuncotationMap {
     /** Standard Logger.  */
     protected static final Logger logger = LogManager.getLogger(FuncotationMap.class);
 
-
     final private Map<String, LinkedHashSet<Funcotation>> txToFuncotations = new LinkedHashMap<>();
 
     private FuncotationMap() {}
@@ -166,6 +165,15 @@ public List<String> getTranscriptList() {
         return new ArrayList<>(txToFuncotations.keySet());
     }
 
+    /**
+     * Get the transcripts as a of transcripts in order.
+     *
+     * @return Never {@code null}
+     */
+    public LinkedHashSet<String> getTranscriptSet() {
+        return new LinkedHashSet<>(txToFuncotations.keySet());
+    }
+
     /** Create a FuncotationMap where all Funcotations will be TableFuncotations.  This is useful for parsing existing
      *   VCFs.
      * Only renders for a single allele.

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotationMapUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotationMapUnitTest.java
@@ -14,6 +14,7 @@
 import org.broadinstitute.hellbender.exceptions.GATKException;
 import org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation;
 import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation;
+import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder;
 import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfCodec;
@@ -513,4 +514,36 @@ public void testCreateNoTranscriptInfo(final List<Funcotation> funcotations) {
         Assert.assertEquals(funcotationMap.getGencodeFuncotations(FuncotationMap.NO_TRANSCRIPT_AVAILABLE_KEY).size(), 0);
     }
 
+    @DataProvider
+    public Object[][] provideFakeGencodeData() {
+
+        return new Object[][] {
+                {Collections.singletonList(new GencodeFuncotationBuilder().setAnnotationTranscript("TXID").build())},
+                {Arrays.asList(new GencodeFuncotationBuilder().setAnnotationTranscript("TXID1").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID2").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID3").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID4").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID5").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID6").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID7").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID8").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID9").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID10").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID11").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID12").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID13").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID14").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID15").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID16").build(),
+                        new GencodeFuncotationBuilder().setAnnotationTranscript("TXID17").build())
+                }
+        };
+    }
+
+    @Test(dataProvider = "provideFakeGencodeData")
+    public void testTranscriptListAndSetAreOrdered(final List<GencodeFuncotation> gencodeFuncotations) {
+        // Tests that both the list and the set are ordered the same way and produce equals values.
+        final FuncotationMap funcotationMap = FuncotationMap.createFromGencodeFuncotations(gencodeFuncotations);
+        Assert.assertEquals(funcotationMap.getTranscriptList(), new ArrayList<>(funcotationMap.getTranscriptSet()));
+    }
 }