Add domain-specific fixes

[RK900]

Things DSP should do after CNN and base structure selector:

Can look at EteRNAbot rules for more strategies.

• Correct base pairings
• Make all bases in loop A's
• Change end pairs to G-C pairs
  • for i in pairmap: get index of last pair before -1, get index of paired base, and change bases at those indices to G-C

• Boosting
  • Hairpins - boost with G
    • if num_unpaired_bases_in_a_row >= 3 then boost with G
  • Internal - boost with opposite G's
    • `if number of unpaired on either side is within +-3, then put Gs on either side
  • Single-bond stack - G-G in the loop
    • for every paired base: if '(' has one '.' following it and its complementary ')' has one '.' preceding it, then G-G boost
  • Bulges
    • http://eternagame.wikia.com/wiki/Zigzag
  • U-G-U-G superboost
    • for every paired base: if '(' has two '.'s following it and its complementary ')' has two '.'s preceding it, then UGUG boost
  • http://eternagame.wikia.com/wiki/Boosting
• If bases aren't pairing correctly:
  • Flip orientation of base pairs nearby
  • Change pairs to G-C pairs

[RK900]

Can run fixer before CNN

• All pairs to A-U
• Boosting

[RK900]

Run this before and after CNN and base fixer.

[RK900]

Fixed in b192939.