Fixed
- implemented logging module
- made read filtering into a saved table
- implemented and tested "filter_reads.get_paired_reads"
- multiprocessing of SNP calling implemented
- setup.py is made; can now install itself
- changed the quoting on CC's table outputs to default
- changed "level" to "filter_cutoff"
- changed "min_coverage" to "min_cov"
- account for read overlap when calculating read length (half code is there, but reverted)
- changed to "no_filter" stepper
- clonality is now called the same with CC and Matt's versions
- min_cov is called with >= now