Redundant UDG flags

[jfy133]

Currently two flags (--udg) and (--udg_type) related to UDG treatment for downstream PMD/BamUtil trimming.

However functionally they pretty much do the same thing, but the latter being more detailed so you can condense into one.

It might also be worth modifying the flag name to --pmd_udg_type so a novice user doesn't add their UDG treatment when they don't in fact want PMD processing.

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[jfy133]

Note: don't even have --udg_treatment

Literally don't even need current --udg type. I think purely --pmd_udg_type [option] should turn on that functionality.