Fixes #4193

`XsvTableFeature` no longer removes an extra column if start and end in
the config file for a `LocatableXsv` data source are the same.

src/main/java/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/XsvTableFeature.java

@@ -77,7 +77,14 @@ public XsvTableFeature(final int contigColumn, final int startColumn, final int
         this.columnValues = columnValues;
 
         // Create our list of indices to remove:
-        locationColumnRemoveIndiciesInOrder = new ArrayList<>(Arrays.asList(contigColumn, startColumn, endColumn));
+        if ( startColumn == endColumn ) {
+            // Don't add the same column more than once:
+            locationColumnRemoveIndiciesInOrder = new ArrayList<>(Arrays.asList(contigColumn, startColumn));
+        }
+        else {
+            locationColumnRemoveIndiciesInOrder = new ArrayList<>(Arrays.asList(contigColumn, startColumn, endColumn));
+        }
+
         locationColumnRemoveIndiciesInOrder.sort(Collections.reverseOrder());
     }
 

src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java

@@ -50,19 +50,22 @@ public class FuncotatorIntegrationTest extends CommandLineProgramTest {
     private static final boolean doDebugTests = false;
     private static final String LARGE_DATASOURCES_FOLDER = "funcotator_dataSources_latest";
 
-    private static final String PIK3CA_VCF_HG19 = toolsTestDir + "funcotator/0816201804HC0_R01C01.pik3ca.vcf";
-    private static final String PIK3CA_VCF_HG38 = toolsTestDir + "funcotator/hg38_trio.pik3ca.vcf";
-    private static final String PIK3CA_VCF_HG19_SNPS = toolsTestDir + "funcotator/PIK3CA_SNPS_3.vcf";
-    private static final String PIK3CA_VCF_HG19_INDELS = toolsTestDir + "funcotator/PIK3CA_INDELS_3.vcf";
-    private static final String MUC16_VCF_HG19 = toolsTestDir + "funcotator/MUC16_MNP.vcf";
-    private static final String PIK3CA_VCF_HG19_ALTS = toolsTestDir + "funcotator/PIK3CA_3_miss_clinvar_alt_only.vcf";
-    private static final String SPANNING_DEL_VCF = toolsTestDir + "funcotator/spanning_del.vcf";
-    private static final String DS_PIK3CA_DIR = largeFileTestDir + "funcotator/small_ds_pik3ca/";
-    private static final String DS_MUC16_DIR = largeFileTestDir + "funcotator/small_ds_muc16/";
-    private static final String MAF_TEST_CONFIG = toolsTestDir + "funcotator/maf.config";
+    private static final String PIK3CA_VCF_HG19          = toolsTestDir + "funcotator" + File.separator + "0816201804HC0_R01C01.pik3ca.vcf";
+    private static final String PIK3CA_VCF_HG38          = toolsTestDir + "funcotator" + File.separator + "hg38_trio.pik3ca.vcf";
+    private static final String PIK3CA_VCF_HG19_SNPS     = toolsTestDir + "funcotator" + File.separator + "PIK3CA_SNPS_3.vcf";
+    private static final String PIK3CA_VCF_HG19_INDELS   = toolsTestDir + "funcotator" + File.separator + "PIK3CA_INDELS_3.vcf";
+    private static final String MUC16_VCF_HG19           = toolsTestDir + "funcotator" + File.separator + "MUC16_MNP.vcf";
+    private static final String PIK3CA_VCF_HG19_ALTS     = toolsTestDir + "funcotator" + File.separator + "PIK3CA_3_miss_clinvar_alt_only.vcf";
+    private static final String SPANNING_DEL_VCF         = toolsTestDir + "funcotator" + File.separator + "spanning_del.vcf";
+    private static final String DS_PIK3CA_DIR            = largeFileTestDir + "funcotator" + File.separator + "small_ds_pik3ca" + File.separator;
+    private static final String DS_MUC16_DIR             = largeFileTestDir + "funcotator" + File.separator + "small_ds_muc16" + File.separator;
+    private static final String MAF_TEST_CONFIG          = toolsTestDir + "funcotator" + File.separator + "maf.config";
+    private static final String XSV_CLINVAR_COL_TEST_VCF = toolsTestDir + "funcotator" + File.separator + "clinvar_hg19_column_test.vcf";
+    private static final String DS_XSV_CLINVAR_COL_TEST  = largeFileTestDir + "funcotator" + File.separator + "small_ds_clinvar_hg19" + File.separator;
 
     private static String hg38Chr3Ref;
     private static String b37Chr3Ref;
+    private static String b37Chr2Ref;
     private static String hg19Chr3Ref;
     private static String hg19Chr19Ref;
 
@@ -78,6 +81,7 @@ public class FuncotatorIntegrationTest extends CommandLineProgramTest {
 
         hg38Chr3Ref = FuncotatorReferenceTestUtils.retrieveHg38Chr3Ref();
         b37Chr3Ref = FuncotatorReferenceTestUtils.retrieveB37Chr3Ref();
+        b37Chr2Ref = FuncotatorReferenceTestUtils.retrieveB37Chr2Ref();
         hg19Chr3Ref = FuncotatorReferenceTestUtils.retrieveHg19Chr3Ref();
         hg19Chr19Ref = FuncotatorReferenceTestUtils.retrieveHg19Chr19Ref();
     }
@@ -425,10 +429,51 @@ public void testCanAnnotateMixedContigHg19Clinvar() {
 
         // Look for "MedGen" to know that we have a clinvar hit.
         Assert.assertEquals(variantContexts.stream()
-                .filter(vc -> StringUtils.contains(vc.getAttributeAsString("FUNCOTATION", ""), "MedGen"))
+                .filter(vc -> StringUtils.contains(vc.getAttributeAsString(VcfOutputRenderer.FUNCOTATOR_VCF_FIELD_NAME, ""), "MedGen"))
                 .count(), NUM_CLINVAR_HITS);
     }
 
+    @Test
+    public void testXsvLocatableAnnotationsHaveCorrectColsForOnlyOnePositionSpecified() {
+        final FuncotatorArgumentDefinitions.OutputFormatType outputFormatType = FuncotatorArgumentDefinitions.OutputFormatType.VCF;
+        final File outputFile = getOutputFile(outputFormatType);
+
+        final ArgumentsBuilder arguments = new ArgumentsBuilder();
+
+        arguments.addVCF(new File(XSV_CLINVAR_COL_TEST_VCF));
+        arguments.addOutput(outputFile);
+        arguments.addReference(new File(b37Chr2Ref));
+        arguments.addArgument(FuncotatorArgumentDefinitions.DATA_SOURCES_PATH_LONG_NAME, DS_XSV_CLINVAR_COL_TEST);
+        arguments.addArgument(FuncotatorArgumentDefinitions.REFERENCE_VERSION_LONG_NAME, FuncotatorTestConstants.REFERENCE_VERSION_HG19);
+        arguments.addArgument(FuncotatorArgumentDefinitions.OUTPUT_FORMAT_LONG_NAME, outputFormatType.toString());
+        arguments.addBooleanArgument(FuncotatorArgumentDefinitions.ALLOW_HG19_GENCODE_B37_CONTIG_MATCHING_LONG_NAME, true);
+
+        runCommandLine(arguments);
+
+        final Pair<VCFHeader, List<VariantContext>> vcfInfo = VariantContextTestUtils.readEntireVCFIntoMemory(outputFile.getAbsolutePath());
+        final VCFInfoHeaderLine funcotationHeaderLine = vcfInfo.getLeft().getInfoHeaderLine(VcfOutputRenderer.FUNCOTATOR_VCF_FIELD_NAME);
+
+        final String[] funcotationFieldNames = FuncotatorUtils.extractFuncotatorKeysFromHeaderDescription(funcotationHeaderLine.getDescription());
+
+        final int EXPECTED_NUM_VARIANTS = 10;
+        Assert.assertEquals(vcfInfo.getRight().size(), EXPECTED_NUM_VARIANTS);
+
+        for (final VariantContext vc : vcfInfo.getRight() ) {
+            final String funcotation = vc.getAttributeAsString(VcfOutputRenderer.FUNCOTATOR_VCF_FIELD_NAME, "");
+
+            Assert.assertNotEquals(funcotation, "");
+
+            final String rawFuncotations = funcotation.substring(1,funcotation.length()-1);
+
+            Assert.assertEquals(StringUtils.countMatches(rawFuncotations, VcfOutputRenderer.FIELD_DELIMITER), funcotationFieldNames.length - 1);
+
+            // This is here to make sure we can create the FuncotationMap object without exploding.
+            // It serves as a secondary check.
+            final FuncotationMap funkyMap = FuncotationMap.createAsAllTableFuncotationsFromVcf(FuncotationMap.NO_TRANSCRIPT_AVAILABLE_KEY, funcotationFieldNames,
+                    funcotation, vc.getAlternateAllele(0), "VCF");
+        }
+    }
+
     @Test
     public void testCanAnnotateHg38ClinvarAndGencodeV28() {
         // Clinvar datasource did  go through one round of preprocessing to make contig names "1" --> "chr1" (for example).  This is an issue with ClinVar, not GATK.

src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorTestConstants.java

@@ -16,6 +16,7 @@ public class FuncotatorTestConstants {
     public static final String HG19_CHR3_REFERENCE_FILE_NAME = GATKBaseTest.largeFileTestDir + "funcotator" + File.separator + "GRCh37.p13.chr3.tar.gz";
     public static final String HG19_3_REFERENCE_FILE_NAME = GATKBaseTest.largeFileTestDir + "funcotator" + File.separator + "b37.3.tar.gz";
     public static final String HG38_3_REFERENCE_FILE_NAME = GATKBaseTest.largeFileTestDir + "funcotator" + File.separator + "hg38.3.tar.gz";
+    public static final String HG19_2_REFERENCE_FILE_NAME = GATKBaseTest.largeFileTestDir + "funcotator" + File.separator + "b37.2.tar.gz";
 
     public static final String FUNCOTATOR_DATA_SOURCES_MAIN_FOLDER = GATKBaseTest.largeFileTestDir + "funcotator" + File.separator + "funcotator_dataSources" + File.separator;
 

src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorReferenceTestUtils.java

@@ -26,12 +26,14 @@ private FuncotatorReferenceTestUtils() {} // Cannot instantiate this class.
     private static Lazy<String> hg19Chr3Ref;
     private static Lazy<String> hg19Chr19Ref;
     private static Lazy<String> b37Chr3Ref;
+    private static Lazy<String> b37Chr2Ref;
     private static Lazy<String> hg38Chr3Ref;
 
     static {
         hg19Chr3Ref = new Lazy<>(createInitializer(new File(FuncotatorTestConstants.HG19_CHR3_REFERENCE_FILE_NAME)));
         hg19Chr19Ref = new Lazy<>(createInitializer(new File(FuncotatorTestConstants.HG19_CHR19_REFERENCE_FILE_NAME)));
         b37Chr3Ref = new Lazy<>(createInitializer(new File(FuncotatorTestConstants.HG19_3_REFERENCE_FILE_NAME)));
+        b37Chr2Ref = new Lazy<>(createInitializer(new File(FuncotatorTestConstants.HG19_2_REFERENCE_FILE_NAME)));
         hg38Chr3Ref = new Lazy<>(createInitializer(new File(FuncotatorTestConstants.HG38_3_REFERENCE_FILE_NAME)));
     }
 
@@ -102,6 +104,11 @@ public static String retrieveHg19Chr19Ref() {
      */
     public static String retrieveB37Chr3Ref() { return b37Chr3Ref.get(); }
 
+    /**
+     * @return a path (as String) to the b37 chromosome 2 only reference.  ("2")
+     */
+    public static String retrieveB37Chr2Ref() { return b37Chr2Ref.get(); }
+
     /**
      * @return a path (as String) to the hg38 chromosome 3 only reference.  ("chr3" in hg38)
      */