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.

Copied script PlottingFunction_SVconsistency/SV_ConsistencyCheck_PlottingFunction.R from strandsequtils repository. Created by Ashley

Update conda environment: this fixes an error "assert_that: assertion must return a logical value", presumably due to a new version of r-assertthat. Also, add scipy (needed for ploidy estimation script) and whatshap (needed for haplotagging).

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.)

Restructured Dockerfile to utilize layers. Also remove external data (BSgenome.Hsapiens.UCSC.hg38) from image - this has to be provided by the user