UngappedKmer now implements Externalizable and has custom read and write object methods.
Created NegativeControlGenerator function. Appears to work correctly, but generating an unlimited number of probes can take a very long time. May want to try to optimize performance a bit.
dramatically improved performance by making chromosome singleton and shortcutting string compareTo() method when comparing a chromosome to itself. NegativeControlGenerator appears to be working correctly. Generating unlimited number of negative control probes very slow, though.