code: def check_mismatches(read, pair, mismatches, mm_option, req_map):
      
      # if read is not paired, make sure it is mapped and that mm <= thresh
      if pair is False:
          mm = count_mismatches(read)
          if mm is False:
              return False
          # if no threshold is supplied, return True
          if mismatches is False:
              return True
          # passes threshold?
          if mm <= mismatches:
              return True
      # paired reads
      r_mm = count_mismatches(read)
      p_mm = count_mismatches(pair)
      # if neither read is mapped, return False
      if r_mm is False and p_mm is False:
          return False
      # if no threshold, return True
      if mismatches is False:
          return True
      # if req_map is True, both reads have to map
      if req_map is True:
          if r_mm is False or p_mm is False:
              return False
      ## if option is 'one,' only one read has to pass threshold
      if mm_option == 'one':
          if (r_mm is not False and r_mm <= mismatches) or (p_mm is not False and p_mm <= mismatches):
              return True
      ## if option is 'both,' both reads have to pass threshold
      if mm_option == 'both':
          ## if one read in pair does not map to the scaffold,
          ## make sure the other read passes threshold
          if r_mm is False:
              if p_mm <= mismatches:
                  return True
          elif p_mm is False:
              if r_mm <= mismatches:
                  return True
          elif (r_mm is not False and r_mm <= mismatches) and (p_mm is not False and p_mm <= mismatches):
              return True
      return False
docs: - check to see if the read maps with <= threshold number of mismatches
      - mm_option = 'one' or 'both' depending on whether or not one or both reads
         in a pair need to pass the mismatch threshold
      - pair can be False if read does not have a pair
      - make sure alignment score is not 0, which would indicate that the read was not aligned to the reference