This fixes issue #1022 of Snakemake (https://bitbucket.org/snakemake/snakemake/issues/1022)

Fixing a Singularity issue with PYTHONPATH (see https://bitbucket.org/snakemake/snakemake/issues/1031)

(works on my computer).

This allows me to more rapidly develp the Dockerfile. Also this commit
includes a separate conda environment which is going to be used within
singularity

Important flag *sn_sites_to_genotype* in the configfile. This overwrites the entry from *Snake.config.json*. The file it points to has to be provided by the user (too big to include into image)

Make reference genome a parameter rather than an input file. This avoids trouble within singularity, where input file existence cannot be checked before the container has been loaded

Copied functionality to select segmentation from detect_strand_states.py into separate script select_segmentation.py, to be used for simulation.