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 an
exit 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