DSL2: PMDTools for estimation vs manipulation of damage

[TCLamnidis]

Now that we separated damage estimation and manipulation, PMDTools would need to be ran twice potentially, once for PMD Filtering and once as a damage estimation tool (if so chosen by the user)

The current options would then fall into two separate categories:

Damage Manipulation

• pmdtools_threshold
• pmdtools_reference_mask (TO be reimplemented within the reference sheet anyway.

Damage Estimation

• pmdtools_range
• pmdtools_max_reads
• pmdtools_platypus