PointFinder breaks on 23S hit

Hi Rolf, thanks for the 4.2 release!

I’m getting the following error with PointFinder. This is with latest pointfinder_db, resfinder from pip (but same from source), against this “unit-test ecoli”: https://kcri.it/test.fa.gz.

Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/opt/conda/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/opt/conda/lib/python3.9/site-packages/resfinder/__main__.py", line 5, in <module>
    sys.exit(main())
  File "/opt/conda/lib/python3.9/site-packages/resfinder/run_resfinder.py", line 451, in main
    results_pnt = PointFinder.discard_unknown_muts(
  File "/opt/conda/lib/python3.9/site-packages/resfinder/cge/pointfinder.py", line 398, in discard_unknown_muts
    known_muts = PointFinder._get_known_mis_matches(
  File "/opt/conda/lib/python3.9/site-packages/resfinder/cge/pointfinder.py", line 414, in _get_known_mis_matches
    f"_{mis_match[8].lower()}")
IndexError: list index out of range

I sprinkled some eprints in the code and this appears to happen once it gets to the 23S hits; the DNA hits process fine. The mis_match array then has only 6 elements (no codon columns?), so the 8 is out of range.

When I patched this out (replacing 8 by -1) pointfinder ran to near the end, but broke on an issue related to phenotype panels. Will report that separately.

Cheees, Marco

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