Accounting for the possibility of a delete-state in function check_for_j. #10
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On occasion, line 744 in anarcy.py (line reading jRegion = [ (state, index+cys_si+1) for state, index in re_states[0] if state[0] >= 117 ]) fails with an error about adding int and NoneType. This is because the value index can end up being None if the current state in the state vector is a delete state (see _hmm_alignment_to_states). I would be very curious to know if you think my fix is correct. Please let me know and hope this helps.