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.

Close to Carlo's original version with bug fixes

Core algorithm identical to v0.1, but with some minor bug fixes in file handling, python 2/3 compatibility, and a few additional scripts for SNP filtering.

Original version by Carlo

This is Carlo's original version, unchanged, with script moved into bin and perl_scripts