Adding util-function to apply custom parameters.
Same SAMTools genotyper customizable.
Add standard test for CLI values.
Fix optimization for single BAM inputs.
Support depths of large BAMs, calculate max depth.

Use genomeCoverageBed to do whole genome depth histograms, thereby
preventing excessive RAM usage. Calculate max depth value that may
be used to filter the most extreme 0.5% of sites.
Split out VCF filter from genotyper.
Major work on phylo pipeline.
Adding standalone tool to calculate BAM depths.
Adding tool to convert GTF to BED.
Merge branch 'master' of github.com:MikkelSchubert/pypeline