Switch from v0.3 to latest git version of C++ code, requires a workaround to fix the bps column of segmentation output.

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.

Add alpha parameter, use --seed option of mosaic simulate, and create link to simulated strand states