Simpler Snakemake pipeline and documentation

What's new

• Improved the Snakemake pipeline
  • Slightly more robust to using custom named sets of regions
  • Updated docker container and link repo with quay.io
  • Added more documentation, including an example to evaluate calls against the GIAB truthset
  • Integrated the scripts used by the Snakemake pipeline into a wrapper function. Now the evaluation can be run more easily as a command-line tool. The Snakemake pipeline is also simpler to use and set up (just need the Snakefile and a config.yaml).
  • Adde a way to define envmodules, for example, to be used in HPC platforms.
• More on the repeat "wiggle room" to help match SVs that might be positioned differently within simple repeats
  • Added documentation
  • Prepareed small input files for GRCh38 and GRCh37.
• Added some documentation for misc functions (frequency annotation, repeat annotation, SV clustering and VCF parsing).
• Improved plot_ranges function
  • SVs are displayed with consistent colors and shapes.
  • No errors when no SVs to plot.
  • Ability to compare to another run
• Tweaked explore_eval_svs to better look at FPs/FNs/TPs