Major overhaul of msitools by Joe:
  - use strict and warning
  - no longer re-write the input file to per-chrom intermediary files
  - read the entire repeat library into memory instead of per-chrom
  - alter indexes when parsing input file to account for new mapQ column
  - add flank_bp parameter; specifies how many bp flanking each side of
    STR must match the reference sequence.
  - general code readability cleanup
  - hopefully no bugs!  UNTESTED!
Rename msitools