Switched to pysam, added new scripts, improved multiprocessing

• Switches sam/bam file processing to pysam from manual processing, obviating
  the need to specify single or paired end in the CountSNPASE step.
• Changed parallelization to use the ASEr/cluster.py library, allowing the use of
  torque, slurm, or simple threading almost transparently.
• Added scripts to automate the creation of source files required for the two main
  pipeline stages.
• A number of small bug fixes.