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.)

Do not install StrandPhaseR! Installation of tools should remain independent of the workflow description