Fix BEDCodec.canDecode() to handle block-compressed extensions (#704)

fix BEDCodec.canDecode to handle block-compressed extensions

src/main/java/htsjdk/tribble/bed/BEDCodec.java

@@ -23,6 +23,7 @@
  */
 package htsjdk.tribble.bed;
 
+import htsjdk.tribble.AbstractFeatureReader;
 import htsjdk.tribble.AsciiFeatureCodec;
 import htsjdk.tribble.annotation.Strand;
 import htsjdk.tribble.index.tabix.TabixFormat;
@@ -40,6 +41,9 @@
  */
 public class BEDCodec extends AsciiFeatureCodec<BEDFeature> {
 
+    /** Default extension for BED files. */
+    public static final String BED_EXTENSION = ".bed";
+
     private static final Pattern SPLIT_PATTERN = Pattern.compile("\\t|( +)");
     private final int startOffsetValue;
 
@@ -197,7 +201,13 @@ private void createExons(int start, String[] tokens, FullBEDFeature gene,
 
     @Override
     public boolean canDecode(final String path) {
-        return path.toLowerCase().endsWith(".bed");
+        final String toDecode;
+        if (AbstractFeatureReader.hasBlockCompressedExtension(path)) {
+            toDecode = path.substring(0, path.lastIndexOf("."));
+        } else {
+            toDecode = path;
+        }
+        return toDecode.toLowerCase().endsWith(BED_EXTENSION);
     }
 
     public int getStartOffset() {

src/test/java/htsjdk/tribble/bed/BEDCodecTest.java

@@ -226,4 +226,15 @@ private void createIndex(File testFile, File idxFile) throws IOException {
     public void testGetTabixFormat() {
         Assert.assertEquals(new BEDCodec().getTabixFormat(), TabixFormat.BED);
     }
+
+    @Test
+    public void testCanDecode() {
+        final BEDCodec codec = new BEDCodec();
+        final String pattern = "filename.%s%s";
+        for(final String bcExt: AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) {
+            Assert.assertTrue(codec.canDecode(String.format(pattern, "bed", bcExt)));
+            Assert.assertFalse(codec.canDecode(String.format(pattern, "vcf", bcExt)));
+            Assert.assertFalse(codec.canDecode(String.format(pattern, "bed.gzip", bcExt)));
+        }
+    }
 }