Prefer os.subprocess.call() to os.system()

[callunity]

Describe the bug

os.system() presents security vulnerabilities. The Python docs indicate that using the subprocess module is preferred.

To Reproduce

See 5 instances of os.system() in ConsensusCruncher.py

Additional considerations

Existing os.subprocess.call invocations in ConsensusCruncher.py create a string and then split it on spaces. This could be dangerous if any of the strings being passed in to the .format() call contain spaces. This could be mitigated by converting lines like this:

call("{} index {}/{}.sorted.bam".format(args.samtools, bam_dir, filename).split(' '))

To:

call([args.samtools, "index", "{}/{}.sorted.bam".format(bam_dir, filename)])