IndexError when processing CRyPTIC samples

[philipwfowler]

I see 113 failures with the following Traceback, VCF attached.

minor_alleles.txt

site.05.subj.PMOP-0632.lab.MOP-197.iso.1.v0.12.4.per_sample.vcf.gz

Traceback (most recent call last):
  File "/home/ubuntu/.local/bin/gnomonicus", line 122, in <module>
    mutations, referenceGenes = populateMutations(vcfStem, options.output_dir, diff,
  File "/home/ubuntu/.local/lib/python3.10/site-packages/gnomonicus/gnomonicus_lib.py", line 388, in populateMutations
    x = minority_population_mutations(diffs, resistanceCatalogue)
  File "/home/ubuntu/.local/lib/python3.10/site-packages/gnomonicus/gnomonicus_lib.py", line 666, in minority_population_mutations
    mutations = diff.minor_populations(interpretation=minor_type)
  File "/home/ubuntu/.local/lib/python3.10/site-packages/gumpy/difference.py", line 839, in minor_populations
    return self.gene2.minority_populations_GARC(interpretation=interpretation, reference=self.gene1)
  File "/home/ubuntu/.local/lib/python3.10/site-packages/gumpy/gene.py", line 217, in minority_populations_GARC
    pos = self.gene_position[self.nucleotide_number == population[0]][0]
IndexError: index 0 is out of bounds for axis 0 with size 0