Update simulator

[pb-cdunn]

Per Gene's request, here are my current changes. I don't expect them to be copied verbatim.

• Allow circular genome.
• Allow user-provided reference.
  • In that case, the RNG seed must be moved.
  • The reference is just a single line of letters, not a true FASTA.
• Allow upper-case input and output. (I don't really care about that though.)
• For my testing, I have 0 indels and no flipping.