From Genome Analysis Wiki
=== Return Value ===
* 0: all records are successfully read and written.
* non-0: an error occurred processing the parameters or reading one of the files.
=== Output Format ===
* ReadName/Fragment combo is in one file, but not in the other file within the window set by recPoolSize & posDiff
* ReadName/Fragment combo is in both files, but at least one of the specified fields to diff is different
== readReference ==