Cluster submission now works for torque and slurm, on any modern system, and can also use the python multiprocessing module if those systems are not present.
Waiting for cluster jobs now based on job completion, _done files only used to check for actual success, so that we can abort on failure.
I pushed a lot of code from the two main scripts to functions, which helps to isolate bugs and improve readability.
Extra scripts added to bin.
Unnecessary command line options and variables removed, particularly those relating to sam file processing, as they were made redundant by pysam.
Altered code to allow running from a different directory
Enable transparent opening of gzipped and b2zipped files.
_donefiles only used to check for actual success, so that we can abort on failure.