1. Increased the size of the bloom filter. In low complexity repeat regions the previous heuristic wasn't working.
 2. Added a --breadth option, that limits the maximum number of paths.
 3. Added a --maxInsert option, that limits the maximum length of a path above the length of the reference sequence. The need for this was partly abrogated by increasing the bloom filter size.
 4. Fixed a bug in initPaths()
 5. Made --ROIqual simply -q and applied that threshhold to realignments as well.