Updated simulation pipeline to support multiple contigs.

* Introduced new dependency to pyfasta, to handle efficient
  handling of fasta files.
* Metasim now produces a reads file for each contig. Updated
  metasim code for this.
* Dwgsim works the same, but made sure its quiet (should be
  printed to log file later on).
* Changed name of create_indel_genome to create_donor_contigs
  since we may not be creating an entire genome.
* Updated pipline script to reflect the changes made to
  create_indel_genome.
Updated documentation with multiple contig support.