docs: def libseq_parse(self, line):
          """This method parses a line containing a lib_seq string and adds it to
          the lib_seq key in the self.params dictionary"""
          count = line.count(',')
          if count > 1:
              raise ValueError("""ERROR: There are too many commas in your
              lib_seq line. There should only be one, between the two filepath
              globs.""")
          if count == 0:
              raise ValueError("""ERROR: There are no commas in your
              lib_seq line. There should be one, between the two filepath
              globs.""")
          line = [x.strip() for x in line.split() if x]
          #print(line)
  
          #This block tries to fix user input if there is an inappropriate
          # number of commas or spaces associated with commas
          if len(line) > 13:
              commas = [x for x in line if "," in x]
              if commas:
                  #this handles the case if there was an extra space added on
                  # both sides of the comma
                  if (len(commas) == 1) and (commas[0] != ','):
                      if (commas[0][-1] == ',') or (commas[0][0] == ','):
                          line = [line[0]] + ["".join(line[1:3])] + line[3:]
                  #This handles the case where there is an extra space on either
                  #side of the comma
                  elif line[2] == ',':
                      line = [line[0]] + ["".join(line[1:4])] + line[4::]
  
          #make sure there is an appropriate numer of elements in list
          if (len(line) ) != 13:
              raise ValueError("""ERROR: There are {0} values in the lib_seq line when
                               there should be 12. Check your input meraculous
                               config file for errors and make sure that it matches
                               the specification for the Meraculous manual.""".format(
                                   len(line)))
  
          for index in self.indices:
              if index == 1:
                  globs = [os.path.abspath(x.strip()) for x in line[1].split(',') if x]
                  #make sure there are only two filepaths to search for globs
                  if len(globs) != 2:
                      raise ValueError("""ERROR: remember to split your glob
                      filepaths in lib_seq with a comma. This error occured because
                      the program was looking for two glob filepaths, but instead
                      found {}: {}""".format(len(globs), globs))
                  self.data["globs"] = globs
                  #Note that glob.glob returns an empty list if the file or glob
                  # filepath does not exist.
                  forwards = glob.glob(os.path.abspath(globs[0]))
                  reverses = glob.glob(os.path.abspath(globs[1]))
                  # print(os.path.abspath(globs[0]))
                  # print("globs: ", globs)
                  # print("forwards: ", forwards)
                  # print("reverses: ", reverses)
                  #At this point the
                  if (len(forwards) < 1) or (len(reverses) < 1):
                      # print("forwards: ", forwards)
                      # print("reverses: ", reverses)
  
                      report = []
                      if len(forwards) < 1:
                          report.append(globs[0])
                      if len(reverses) < 1:
                          report.append(globs[1])
                      raise ValueError("""ERROR: no read files were found for the glob strings,
                      {}.
  
                      Please check the glob string and/or use absolute
                      file paths. A common source of this error is using
                      relative filepaths from the incorrect directory, or
                      referring to files that do not exist.""".format(report))
                  if len(forwards) != len(reverses):
                      raise ValueError("""ERROR: the number of reverse read files does not
                      match the number of forward read files""")
                  #zip the pairs together into tuples, not lists
                  self.data["pairs"] = [x for x in zip(sorted(forwards), sorted(reverses))]
  
              self.data[self.indices.get(index)] = line[index]