typo had messed up the 'False'

Fixed edge case where proteins near the end of the genome that needed to be shifted to the left would break. (when the submitted sequence is shorter than the reference sequence and the last protein is close to the end of the genome). This update also implemented the weird false typo from commit [7e41b87](rcs333@7e41b87)

hopefully incomplete genomes are working again. Moved the catch for if where the adjusted gene stop codon is off the end of the submitted genome to the end of the function to eliminate false positives but keep handling that edge case correctly

Fixed another typo in the adjust function that was checking the wrong value to see if the new gene location was off the end of the genome. Should be working correctly now.

Swapped raw_input for input. No other changes necessary :D

still just ribosomal slippage in orf1ab so no code changes necessary.

Will link picture in readme

Uploaded picture of expected output from a successful run

The --f flag wasn't pulling correct nucleotide sequence for the local reference the user provided, this has now been fixed.

The --f flag wasn't pulling correct nucleotide sequence for the local reference the user provided, this has now been fixed.