Merge pull request #522 from tomwhite/expose-end-of-block-for-bgzf

Add a method to expose whether the stream is positioned at the end of a BGZF block.

Author: akiezun

src/java/htsjdk/samtools/util/BlockCompressedInputStream.java

@@ -132,6 +132,14 @@ public int available()
         return mCurrentBlock.length - mCurrentOffset;
     }
 
+    /**
+     * @return <code>true</code> if the stream is at the end of a BGZF block,
+     * <code>false</code> otherwise.
+     */
+    public boolean endOfBlock() {
+        return (mCurrentBlock != null && mCurrentOffset == mCurrentBlock.length);
+    }
+
     /**
      * Closes the underlying InputStream or RandomAccessFile
      */

src/tests/java/htsjdk/samtools/util/BlockCompressedOutputStreamTest.java

@@ -63,6 +63,14 @@ public void testBasic() throws Exception {
         for(int i = 0; (line = reader.readLine()) != null; ++i) {
             Assert.assertEquals(line + "\n", linesWritten.get(i));
         }
+
+        final BlockCompressedInputStream bcis2 = new BlockCompressedInputStream(f);
+        int available = bcis2.available();
+        Assert.assertFalse(bcis2.endOfBlock(), "Should not be at end of block");
+        Assert.assertTrue(available > 0);
+        byte[] buffer = new byte[available];
+        Assert.assertEquals(bcis2.read(buffer), available, "Should read to end of block");
+        Assert.assertTrue(bcis2.endOfBlock(), "Should be at end of block");
     }
 
     @Test