Index out of range when checking NS5b coverage

[donkirkby]

If the MIDI sample gets rejected for low coverage, then the whole genome sample will fail when it tries to check coverage at resistance positions. The problem is that the list of aminos only goes to position 336 when MIDI is rejected.

Here's the error:

Traceback (most recent call last):
  File "/opt/micall/micall_kive_resistance.py", line 62, in <module>
    main()
  File "/opt/micall/micall_kive_resistance.py", line 59, in main
    sample_group.process_resistance(RunInfo([sample_group]))
  File "/opt/micall/micall/drivers/sample_group.py", line 47, in process_resistance
    resistance_consensus_csv=resistance_consensus_csv)
  File "/opt/micall/micall/resistance/resistance.py", line 545, in report_resistance
    filtered_aminos = filter_aminos(aminos, algorithms)
  File "/opt/micall/micall/resistance/resistance.py", line 273, in filter_aminos
    all_aminos = list(all_aminos)
  File "/opt/micall/micall/resistance/resistance.py", line 251, in read_aminos
    all(aminos[pos-1] for pos in midi_positions))
  File "/opt/micall/micall/resistance/resistance.py", line 251, in <genexpr>
    all(aminos[pos-1] for pos in midi_positions))
IndexError: list index out of range