FULL PRODUCT VERSION :
java version "1.6.0_21"
Java(TM) SE Runtime Environment (build 1.6.0_21-b07)
Java HotSpot(TM) 64-Bit Server VM (build 17.0-b17, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows [Version 6.1.7601]

A DESCRIPTION OF THE PROBLEM :
The following unit test snippet fails as is:

// a) InputStream is = new FileInputStream(f1);
InputStream is = new GZIPInputStream(new FileInputStream(f1));
try {
	do {
		//Skip
		if (is.available() > 0) {
			assertTrue(is.read() != -1);
		} else {
			assertTrue(is.read() == -1);
			assertTrue(is.available() == 0);
			break;
		}
		
	} while (true);

} finally {
	is.close();
}

If we uncomment a) and comment the line after it, the test passes.
1) This hints a possible inconsistency between the input stream and the gzip-wrapped input stream.
2) According to the documentation, when available() tells we have something to take it returns a non-zero value, and a subsequent read() gives a byte from that something. This seems broken at the end of gzipped streams.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run the unit test, completing it with supplying a gzipped file.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Test passes.
ACTUAL -
Test fails.

ERROR MESSAGES/STACK TRACES THAT OCCUR :
Test fails at
	assertTrue(is.read() != -1);

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
@Test
public final void testGzippedStreamAPIConsistency() throws IOException {
	File f1 = new File("bla01.gz");
	writeOperationsZipFile(f1, 20);
		
	// a) InputStream is = new FileInputStream(f1);
	InputStream is = new GZIPInputStream(new FileInputStream(f1));
	try {
		do {
			//Skip
			if (is.available() > 0) {
				assertTrue(is.read() != -1);
			} else {
				assertTrue(is.read() == -1);
				assertTrue(is.available() == 0);
				break;
			}
				
		} while (true);
		
	} finally {
		is.close();
	}
}

private void writeOperationsZipFile(File f, final int howMany) throws IOException {
	OutputStream fos = new GZIPOutputStream(new FileOutputStream(f));
	try {
		writeOutputStream(fos, howMany);
	} finally {
		fos.close();
	}
}
private void writeOutputStream(OutputStream fos, int howMany) {
	PrintStream ps = new PrintStream(fos);
	
	try {
		int i = 0;
		while (i < howMany) {
			//write an operation.
			ps.println("operation" + i);
			i++;
		}//while
	} finally {
		ps.close();
	}
}

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Do not rely on available() but on the return result of read().