DbSnpBitSetUtil should verify that the VCF dict should match the inpu…

src/main/java/picard/util/DbSnpBitSetUtil.java

@@ -32,6 +32,7 @@
 import htsjdk.variant.vcf.VCFFileReader;
 import picard.nio.PicardHtsPath;
 import picard.vcf.ByIntervalListVariantContextIterator;
+import picard.util.SequenceDictionaryUtils;
 
 import java.io.File;
 import java.nio.file.Path;
@@ -213,6 +214,14 @@ private static void loadVcf(final PicardHtsPath dbSnpFile,
 
         final Optional<ProgressLogger> progress = log.map(l -> new ProgressLogger(l, (int) 1e5, "Read", "variants"));
         final VCFFileReader variantReader = new VCFFileReader(dbSnpFile.toPath(), intervals != null);
+
+        SequenceDictionaryUtils.assertSequenceDictionariesEqual(
+            variantReader.getFileHeader().getSequenceDictionary(),
+            "DBSNP: " + dbSnpFile.getRawInputString(),
+            sequenceDictionary,
+            "INPUT"
+        );
+
         final Iterator<VariantContext> variantIterator;
         if (intervals != null) {
             variantIterator = new ByIntervalListVariantContextIterator(variantReader, intervals);

src/test/java/picard/util/SequenceDictionaryUtilsTest.java

@@ -2,10 +2,12 @@
 
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.variant.utils.SAMSequenceDictionaryExtractor;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 import picard.PicardException;
 
+import java.io.File;
 import java.util.List;
 
 public class SequenceDictionaryUtilsTest {
@@ -45,4 +47,35 @@ public void testSequenceDictionaryNegative(final SAMSequenceDictionary s1, final
         SequenceDictionaryUtils.assertSequenceDictionariesEqual(s1, "s1", s2, "s2");
     }
 
-}
+    @Test
+    public void testDbSnpSequenceDictionaryPositive() {
+        final File f1 = new File("testdata/picard/vcf", "mini.dbsnp.vcf");
+        final File f2 = new File("testdata/picard/vcf", "mini.vcf");
+
+        final SAMSequenceDictionary s1 = SAMSequenceDictionaryExtractor.extractDictionary(f1.toPath());
+        final SAMSequenceDictionary s2 = SAMSequenceDictionaryExtractor.extractDictionary(f2.toPath());
+
+        SequenceDictionaryUtils.assertSequenceDictionariesEqual(
+            s1,
+            "s1",
+            s2,
+            "s2"
+        );
+    }
+
+    @Test(expectedExceptions = PicardException.class)
+    public void testDbSnpSequenceDictionaryNegative() {
+        final File f1 = new File("testdata/picard/vcf", "mini.dbsnp.vcf");
+        final File f2 = new File("testdata/picard/vcf", "spanningDeletionCallset.vcf");
+
+        final SAMSequenceDictionary s1 = SAMSequenceDictionaryExtractor.extractDictionary(f1.toPath());
+        final SAMSequenceDictionary s2 = SAMSequenceDictionaryExtractor.extractDictionary(f2.toPath());
+
+        SequenceDictionaryUtils.assertSequenceDictionariesEqual(
+            s1,
+            "s1",
+            s2,
+            "s2"
+        );
+    }
+}