Just a few fixes, also added two flavours of scripts for merging coverage files (e.g. for when R1 and R2 had been run in single-end mode)

Bismark

• removed anexit 0 that would terminate runs after processing a single (set of) input file(s).

deduplicate_bismark

• Changed the path to Samtools to custom variable (#609)

coverage2cytosine

• set threshold reads to 1 (if it was 0) for--gc_context as intended and mentioned in the help text. Fixes#621