Update mask_short_sequences.py

[lcoombe]

Incorporating some changes requested by Rene (upper-casing on ends), and also some changes I made previously in this script.

• Always upper-case k bp on each end
• Added hard-mask option

[lcoombe]

Looks good Lauren, thank you for the changes! Sorry for the delay on this, I must've missed the notification when you opened this PR.

No worries! :) They're not urgent changes or anything, we just figured might as well have the most up-to-date version of the script on the repo!