Now non-locatable data sources can create funcotations again.

scripts/funcotator/testing/testFuncotator.sh

@@ -292,7 +292,7 @@ if [[ $r -eq 0 ]] && ${doRunLargeTests} ; then
     #INPUT=/Users/jonn/Development/gatk/src/test/resources/large/funcotator/regressionTestVariantSet2.vcf
     #INPUT=/Users/jonn/Development/gatk/src/test/resources/large/funcotator/regressionTestHg19Large.vcf
     #INPUT=/Users/jonn/Development/gatk/hg38_trio_liftoverb37.vcf
-    #INPUT=/Users/jonn/Development/gatk/tmp.vcf
+    INPUT=/Users/jonn/Development/gatk/tmp.vcf
     #INPUT=/Users/jonn/Development/gatk/tmp2.vcf
     #INPUT=/Users/jonn/Development/data_to_run/problem_samples/splice_site_should_not_be_splice_site/error_case.vcf
 

src/main/java/org/broadinstitute/hellbender/tools/funcotator/DataSourceFuncotationFactory.java

@@ -135,6 +135,12 @@ public String getVersion() {
         return version;
     }
 
+    /**
+     * @return {@code True} if this {@link DataSourceFuncotationFactory} requires features to create {@link Funcotation}s.  {@code False} otherwise.
+     */
+    @VisibleForTesting
+    public boolean requiresFeatures() { return true; }
+
     /**
      * @return An ordered {@link LinkedHashSet} of the names of annotations that this Data Source supports.
      */
@@ -169,10 +175,20 @@ public List<Funcotation> createFuncotations(final VariantContext variant, final
         Utils.nonNull(referenceContext);
         Utils.nonNull(featureContext);
 
+        final List<Funcotation> outputFuncotations;
+
         // Query this funcotation factory to get the list of overlapping features.
-        final List<Feature> featureList = queryFeaturesFromFeatureContext(featureContext);
+        // NOTE: This will only get features that are LOCATABLE!
+        //       This corresponds to requiresFeatures() returning `True`.
+        final List<Feature> featureList;
 
-        final List<Funcotation> outputFuncotations;
+        // Only get features if we need them:
+        if ( requiresFeatures() ) {
+            featureList = queryFeaturesFromFeatureContext(featureContext);
+        }
+        else {
+            featureList = Collections.emptyList();
+        }
 
         // If our featureList is compatible with this DataSourceFuncotationFactory, then we make our funcotations:
         if ( isFeatureListCompatible(featureList) ) {
@@ -203,12 +219,22 @@ public List<Funcotation> createFuncotations(final VariantContext variant, final
      * Checks to see if the given featureList is compatible with this {@link DataSourceFuncotationFactory}.
      * Cues off of the feature type in the feature list and whether the given list contains any non-null features.
      * This method acts as a sanity-check before attempting to do any annotations on features.
+     * If this {@link DataSourceFuncotationFactory} does not require features as per {@link #requiresFeatures()}, then
+     * this method will always return {@code True}.
      * @param featureList {@link List} of {@link Feature} that might be applicable to this {@link DataSourceFuncotationFactory} for annotation.
      * @return {@code true} if the given {@code featureList} contains at least one non-null feature of type {@link #getAnnotationFeatureClass()}; {@code false} otherwise.
      */
     private boolean isFeatureListCompatible(final List<Feature> featureList) {
-        // Make sure these features can be annotated by this DataSourceFuncotationFactory:
+        // Make sure these features can be annotated by this DataSourceFuncotationFactory.
         // NOTE: We only check the first non-null element of the list for feature type:
+
+        // The feature list is compatible if we found a compatible feature
+        // OR
+        // if this DataSourceFuncotationFactory does not require features.
+        if ( !requiresFeatures() ) {
+            return true;
+        }
+
         boolean foundCompatibleFeature = false;
         for ( final Feature f : featureList ) {
             if (f != null) {

src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/cosmic/CosmicFuncotationFactory.java

@@ -202,6 +202,15 @@ public String getName() {
         return name;
     }
 
+    @Override
+    /**
+     * {@inheritDoc}
+     * Since {@link CosmicFuncotationFactory} primarily keys off a gene name, we don't actually need
+     * any features to create annotations.
+     */
+    @VisibleForTesting
+    public boolean requiresFeatures() { return false; }
+
     @Override
     public LinkedHashSet<String> getSupportedFuncotationFields() {
         return supportedFields;
@@ -250,7 +259,7 @@ protected List<Funcotation> createFuncotationsOnVariant(final VariantContext var
         // Then query our DB for matches on the gene name.
         // Then grab Genome position / Protein position and see if we overlap.
         // If any do, we create our CosmicFuncotation
-        for (  final GencodeFuncotation gencodeFuncotation : gencodeFuncotations ) {
+        for ( final GencodeFuncotation gencodeFuncotation : gencodeFuncotations ) {
             final String geneName = gencodeFuncotation.getHugoSymbol();
 
             final SimpleInterval genomePosition = new SimpleInterval(variant.getContig(), variant.getStart(), variant.getEnd());

src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/xsv/SimpleKeyXsvFuncotationFactory.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv;
 
+import com.google.common.annotations.VisibleForTesting;
 import htsjdk.tribble.Feature;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
@@ -177,6 +178,15 @@ public String getName() {
         return name;
     }
 
+    @Override
+    /**
+     * {@inheritDoc}
+     * Since {@link SimpleKeyXsvFuncotationFactory} keys off a gene name or transcript ID, we don't actually need
+     * any features to create annotations.
+     */
+    @VisibleForTesting
+    public boolean requiresFeatures() { return false; }
+
     @Override
     public LinkedHashSet<String> getSupportedFuncotationFields() {
         return new LinkedHashSet<>(annotationColumnNames);

src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/cosmic/CosmicFuncotationFactoryUnitTest.java

@@ -221,6 +221,11 @@ private Object[][] provideForTestCreateFuncotations() {
     //==================================================================================================================
     // Tests:
 
+    @Test
+    public void testRequiresFeatures() {
+        Assert.assertFalse(new CosmicFuncotationFactory(PATH_TO_TEST_DB).requiresFeatures());
+    }
+
     @Test(dataProvider = "provideDataForTestProteinPositionRegex")
     public void testPositionRegex(final Pattern regex, final List<String> dbPositions, final int expectedNumResults) {
 

src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java

@@ -2503,4 +2503,9 @@ public void testCreateFuncotationsWithFlanks(final String expectedGeneName,
             Assert.assertEquals(funcotation.getHugoSymbol(), expectedGeneName, "Gene name not correct");
         }
     }
+
+    @Test
+    public void testRequiresFeatures() {
+        Assert.assertTrue(testMuc16SnpCreateFuncotationsFuncotationFactory.requiresFeatures());
+    }
 }

src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/vcf/VcfFuncotationFactoryUnitTest.java

@@ -191,6 +191,11 @@ public void testGetAnnotationFeatureClass() {
         Assert.assertEquals(vcfFuncotationFactory.getAnnotationFeatureClass(), VariantContext.class);
     }
 
+    @Test
+    public void testRequiresFeatures() {
+        Assert.assertTrue(createVcfFuncotationFactory(FACTORY_NAME, FACTORY_VERSION, IOUtils.getPath(FuncotatorTestConstants.VARIANT_FILE_HG19_CHR3)).requiresFeatures());
+    }
+
     @Test
     public void testGetType() {
         final VcfFuncotationFactory vcfFuncotationFactory = createVcfFuncotationFactory(FACTORY_NAME, FACTORY_VERSION, IOUtils.getPath(FuncotatorTestConstants.VARIANT_FILE_HG19_CHR3));

src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/xsv/LocatableXsvFuncotationFactoryUnitTest.java

@@ -248,6 +248,11 @@ private Object[][] provideForTestSetSupportedFuncotationFields() {
     //==================================================================================================================
     // Tests:
 
+    @Test
+    public void testRequiresFeatures() {
+        Assert.assertTrue(new LocatableXsvFuncotationFactory(LocatableXsvFuncotationFactory.DEFAULT_NAME, DataSourceFuncotationFactory.DEFAULT_VERSION_STRING, new LinkedHashMap<>(), null).requiresFeatures());
+    }
+
     @Test(dataProvider = "provideForTestGetName")
     public void testGetName(final String name, final String expected) {
         final LocatableXsvFuncotationFactory locatableXsvFuncotationFactory;

src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/xsv/SimpleKeyXsvFuncotationFactoryUnitTest.java

@@ -7,14 +7,14 @@
 import org.broadinstitute.hellbender.engine.ReferenceContext;
 import org.broadinstitute.hellbender.engine.ReferenceDataSource;
 import org.broadinstitute.hellbender.exceptions.GATKException;
+import org.broadinstitute.hellbender.testutils.FuncotatorReferenceTestUtils;
 import org.broadinstitute.hellbender.tools.funcotator.Funcotation;
 import org.broadinstitute.hellbender.tools.funcotator.FuncotatorTestConstants;
 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.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
-import org.broadinstitute.hellbender.testutils.FuncotatorReferenceTestUtils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -425,4 +425,18 @@ public void testCreateFuncotationsIgnoresTranscriptVersions() {
         final TableFuncotation tableFuncotation = (TableFuncotation)funcotation;
         Assert.assertEquals(tableFuncotation.get(defaultName + "_Beatle"), "Harrison", "Wrong value for the Beatle column in returned funcotation");
     }
+
+    @Test
+    public void testRequiresFeatures() {
+        final SimpleKeyXsvFuncotationFactory simpleKeyXsvFuncotationFactory = new SimpleKeyXsvFuncotationFactory(
+                defaultName,
+                IOUtils.getPath(FuncotatorTestConstants.XSV_CSV_FILE_PATH),
+                "VERSION",
+                ",",
+                0,
+                SimpleKeyXsvFuncotationFactory.XsvDataKeyType.GENE_NAME
+        );
+
+        Assert.assertFalse(simpleKeyXsvFuncotationFactory.requiresFeatures());
+    }
 }