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

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)