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)

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

Switch from v0.3 to latest git version of C++ code, requires a workaround to fix the bps column of segmentation output.

Decrease cutoff for adding an extra SCE from 20Mb to 5Mb. Should help avoiding wrong inversion calls towards the end of a chromosome.

Run StrandPhaseR separately for each segmentation parameter set; this is necessary since the segmentation calls affect strand states / SCE calls.