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

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

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

Added rules to re-genotype a set of given SNVs (e.g. from 1000G) and to do haplotagging of BAM files. Slightly reorganized input file structure: now expect two separate folders "bam/{sample}/selected" and "bam/{sample}/all", where "selected" should contain the good Strand-seq libraries, where all should contain all libraries that can be used for SNV calling/genotyping.

Re-activate installation of StrandPhaseR in Snakefile. Otherwise the pipeline doesn't work with the bioconda environment. (I hope that this doesn't have side effects on the Singularity workflow.)