Make stream seek error message informative (#927)

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

@@ -57,10 +57,12 @@
     public final static String INCORRECT_HEADER_SIZE_MSG = "Incorrect header size for file: ";
     public final static String UNEXPECTED_BLOCK_LENGTH_MSG = "Unexpected compressed block length: ";
     public final static String PREMATURE_END_MSG = "Premature end of file: ";
-    public final static String CANNOT_SEEK_STREAM_MSG = "Cannot seek on stream based file ";
+    public final static String CANNOT_SEEK_STREAM_MSG = "Cannot seek a position for a non-file stream";
+    public final static String CANNOT_SEEK_CLOSED_STREAM_MSG = "Cannot seek a position for a closed stream";
     public final static String INVALID_FILE_PTR_MSG = "Invalid file pointer: ";
 
     private InputStream mStream = null;
+    private boolean mIsClosed = false;
     private SeekableStream mFile = null;
     private byte[] mFileBuffer = null;
     private DecompressedBlock mCurrentBlock = null;
@@ -222,6 +224,9 @@ public void close() throws IOException {
         // Encourage garbage collection
         mFileBuffer = null;
         mCurrentBlock = null;
+
+        // Mark as closed
+        mIsClosed = true;
     }
 
     /**
@@ -344,12 +349,20 @@ public int read(final byte[] buffer, int offset, int length) throws IOException
      * Seek to the given position in the file.  Note that pos is a special virtual file pointer,
      * not an actual byte offset.
      *
-     * @param pos virtual file pointer
+     * @param pos virtual file pointer position
+     * @throws IOException if stream is closed or not a file based stream
      */
     public void seek(final long pos) throws IOException {
+        // Must be before the mFile == null check because mFile == null for closed files and streams
+        if (mIsClosed) {
+            throw new IOException(CANNOT_SEEK_CLOSED_STREAM_MSG);
+        }
+
+        // Cannot seek on streams that are not file based
         if (mFile == null) {
             throw new IOException(CANNOT_SEEK_STREAM_MSG);
         }
+
         // Decode virtual file pointer
         // Upper 48 bits is the byte offset into the compressed stream of a
         // block.

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

@@ -81,6 +81,7 @@ public void testBasic() throws Exception {
         Assert.assertEquals(bcis2.read(buffer), available, "Should read to end of block");
         Assert.assertTrue(bcis2.endOfBlock(), "Should be at end of block");
         bcis2.close();
+        Assert.assertEquals(bcis2.read(buffer), -1, "Should be end of file");
     }
 
     @DataProvider(name = "seekReadExceptionsData")
@@ -89,24 +90,32 @@ public void testBasic() throws Exception {
         return new Object[][]{
                 {HTSJDK_TRIBBLE_RESOURCES + "vcfexample.vcf.truncated.gz", FileTruncatedException.class,
                         BlockCompressedInputStream.PREMATURE_END_MSG + System.getProperty("user.dir") + "/" +
-                                HTSJDK_TRIBBLE_RESOURCES + "vcfexample.vcf.truncated.gz", true, false, 0},
+                                HTSJDK_TRIBBLE_RESOURCES + "vcfexample.vcf.truncated.gz", true, false, false, 0},
                 {HTSJDK_TRIBBLE_RESOURCES + "vcfexample.vcf.truncated.hdr.gz", IOException.class,
                         BlockCompressedInputStream.INCORRECT_HEADER_SIZE_MSG + System.getProperty("user.dir") + "/" +
-                                HTSJDK_TRIBBLE_RESOURCES + "vcfexample.vcf.truncated.hdr.gz", true, false, 0},
+                                HTSJDK_TRIBBLE_RESOURCES + "vcfexample.vcf.truncated.hdr.gz", true, false, false, 0},
                 {HTSJDK_TRIBBLE_RESOURCES + "vcfexample.vcf.gz", IOException.class,
-                        BlockCompressedInputStream.CANNOT_SEEK_STREAM_MSG, false, true, 0},
+                        BlockCompressedInputStream.CANNOT_SEEK_STREAM_MSG, false, true, false, 0},
+                {HTSJDK_TRIBBLE_RESOURCES + "vcfexample.vcf.gz", IOException.class,
+                        BlockCompressedInputStream.CANNOT_SEEK_CLOSED_STREAM_MSG, false, true, true, 0},
                 {HTSJDK_TRIBBLE_RESOURCES + "vcfexample.vcf.gz", IOException.class,
                         BlockCompressedInputStream.INVALID_FILE_PTR_MSG + 1000 + " for " + System.getProperty("user.dir") + "/" +
-                                HTSJDK_TRIBBLE_RESOURCES + "vcfexample.vcf.gz", true, true, 1000 }
+                                HTSJDK_TRIBBLE_RESOURCES + "vcfexample.vcf.gz", true, true, false, 1000 }
         };
     }
 
     @Test(dataProvider = "seekReadExceptionsData")
-    public void testSeekReadExceptions(final String filePath, final Class c, final String msg, final boolean isFile, final boolean isSeek, final int pos) throws Exception {
+    public void testSeekReadExceptions(final String filePath, final Class c, final String msg, final boolean isFile, final boolean isSeek, final boolean isClosed,
+                                       final int pos) throws Exception {
 
         final BlockCompressedInputStream bcis = isFile ?
                 new BlockCompressedInputStream(new File(filePath)) :
                 new BlockCompressedInputStream(new FileInputStream(filePath));
+
+        if ( isClosed ) {
+            bcis.close();
+        }
+
         boolean haveException = false;
         try {
             if ( isSeek ) {
@@ -212,5 +221,6 @@ public Deflater makeDeflater(final int compressionLevel, final boolean gzipCompa
         }
         bcis.close();
         Assert.assertEquals(deflateCalls[0], 3, "deflate calls");
+        Assert.assertEquals(reader.readLine(), null);
     }
 }