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)

Add one more SCE after initial assignment, if it improves concordance. Add more than one if necessary to render the assignment valid.

Script for improved SCE calling based on comparing single-cell segmentations to multi-cell segmentations

Upgrade environment to get WhatsHap 0.17, which correctly handles haplotagging when chromosomes are missing in VCF file

Add means to narrow down the number of considered genotypes (a bit less drastic than forcing biallelic); apply haplotag probabilities only after that