Question

I have a file that my Java application takes as input which I read 6 bytes at a time. When I read it in off the file system everything works fine. If I build everything into a jar the first 4868 reads work fine, but after that it starts returning the byte arrays in the wrong order and also ends up having read more data at the end.

Here is a simplified version of my code which reproduces the problem:

     InputStream inputStream = this.getClass().getResourceAsStream(filePath);
     byte[] byteArray = new byte[6];
     int counter = 0;
     while ((inputStream.read(byteArray) != -1))
     {
        counter++;
        System.out.println("Read #" + counter +": " + Arrays.toString(byteArray));
     }
     System.out.println("Done.");

This is the [abbreviated] output I get when reading off of the file system:

...
Read #4867: [5, 0, 57, 7, 113, -26]
Read #4868: [2, 0, 62, 7, 114, -26]
Read #4869: [2, 0, 68, 7, 115, -26]
Read #4870: [3, 0, 75, 7, 116, -26]
Read #4871: [2, 0, 83, 7, 117, -26]
...
Read #219687: [1, 0, 4, -8, 67, 33]
Read #219688: [1, 0, 2, -8, 68, 33]
Read #219689: [5, 0, 1, -8, 67, 33]
Done.

And here is what I get reading from a jar:

...
Read #4867: [5, 0, 57, 7, 113, -26]
Read #4868: [2, 0, 62, 7, 113, -26] //everything is fine up to this point
Read #4869: [7, 114, -26, 2, 0, 68]
Read #4870: [7, 115, -26, 3, 0, 75]
Read #4871: [7, 116, -26, 2, 0, 83]
...
Read #219687: [95, 33, 1, 0, 78, -8]
Read #219688: [94, 33, 1, 0, 76, -8]
Read #219689: [95, 33, 1, 0, 74, -8]
...
Read #219723: [67, 33, 1, 0, 2, -8]
Read #219724: [68, 33, 5, 0, 1, -8]
Read #219725: [67, 33, 5, 0, 1, -8]
Done.

I unzipped the jar and confirmed that the files being read are identical, so what could cause the reader to return different results?

Answer 1

Your reading loop is wrong.
inputStream.read() method returns number of bytes it really read. You have to check this number before transforming the data into string.

When you are reading from file the bytes are not arrived all together. At one of the iterations of your loop you probably read 4 of expected 6 bytes, so your transformation to string does not work.
If you are reading integers I’d recommend you to wrap your raw input string using Scanner or good old DataInputStream and read integers directly.