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.

Update conda environment and include packages r-pheatmap, bioconductor-complexheatmap, and r-gplots needed by plot-clustering.R

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.