Add an option to discard orphans to all trimming tools

[samhunter]

If any trimming tool removes enough bases that a read would be discarded, have the option of discarding the other read in the pair as well. This will allow the user to know that all reads are paired if needed.

[dstreett]

Hey, @samhunter, here is a temporary fix for this issue.

q-window-trim . . . | awk -F '\t' '{ if (NF>=5) print $0; }' | overlapper . . .

[dstreett]

This feature is to be added to - Cut-Trim, PolyAT-Trim, Q-Window-Trim, N-Remover.

[samhunter]

Does the OrphanDiscard branch install executables? It doesn't appear to on my end, but maybe I am doing something silly?

[msettles]

Think this is working, closing for now, reopen if not after further testing