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.

Added options --whitelist and --min_whitelist_interval_size to fine-tune blacklist by whitelisting known SV sites

made with information from the UCSC TableBrowser