How are gaps to be represented (formating) in the strings? ('-' creates an error)

[mantzaris]

using the '-' creates an error which is common to represent a gap. It is in my data and is understandable if there is no point in keeping the '-' since they will be introduced later on by the algorithm, but just wanting to know if there is another convention

>>> alignment = aligner.align(reference="ACGTGAGAATTATGGCGCTGTGATT", query="ACGTGGAATTATGCGCTGGATT--")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/cool/.local/lib/python2.7/site-packages/ssw/sswobj.py", line 112, in align
    res = self._align(query, reference, flags, filter_score, filter_distance, mask_length)
  File "/home/cool/.local/lib/python2.7/site-packages/ssw/sswobj.py", line 121, in _align
    _query = self.matrix.convert_sequence_to_ints(query)
  File "/home/cool/.local/lib/python2.7/site-packages/ssw/sswobj.py", line 70, in convert_sequence_to_ints
    _seq_instance[idx] = self.symbol_map[symbol]
KeyError: '-'