Updated comment about sputnik
Add Sputnik's source and the executable used for this analysis
Rename corrupted bulk_cortex files
Save the exact sputnik executable used
README update
Another major msitools overhaul.  The previous version was incorrect, because it did not account for chromosome when traversing the combined repeat database.
Move from hash-based repeat database to array based for speed.  Also output lines with no supporting reads to make joining easier downstream.