Added support for specifying read error rate in simulator.

* Refactored svsim_pipeline.py to add arguments from
  create_donor_contigs.py and simulatre_reads.py as argument groups,
  so that the pipeline does not need to be changed every time new
  arguments are added.
* Updated dwgsim.py to support read error rates, also remove indels from
  simulation. Since we use the Illumina error model definitions we cannot
  support this in metasim right now.
Added logging output that captures the output from bwa and the read simulators.