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

made with information from the UCSC TableBrowser

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

Script to plot SV calls, copied from github.com:friendsofstrandseq/mosaicatcher/R/chrom.R (having it here allows local, coordinated changes)

Pipeline update to use the new SCE detection and segmentation selected (implemented in utils/detect_strand_states.py)