Change to tb-profiler output

[jodyphelan]

Just thought I'd let you know of a change I've made in v6.6.0 to more closely align with the WHO catalogue.

I've implemented a new rule which will assign "Uncertain significance" to mutations not found in the WHO catalogue. These mutations previous had an empty "annotations" list and now look like this:

{
      "chrom": "Chromosome",
      "pos": 490655,
      "ref": "T",
      "alt": "C",
      "depth": 57,
      "freq": 1,
      "sv": false,
      "filter": "pass",
      "forward_reads": 28,
      "reverse_reads": 29,
      "sv_len": null,
      "gene_id": "Rv0407",
      "gene_name": "fgd1",
      "feature_id": "CCP43138",
      "type": "upstream_gene_variant",
      "change": "c.-128T>C",
      "nucleotide_change": "c.-128T>C",
      "protein_change": "",
      "annotation": [
        {
          "type": "who_confidence",
          "drug": "clofazimine",
          "confidence": "Uncertain significance",
          "comment": "Not found in WHO catalogue",
          "source": "",
          "original_mutation": ""
        },
        {
          "type": "who_confidence",
          "drug": "delamanid",
          "confidence": "Uncertain significance",
          "comment": "Not found in WHO catalogue",
          "source": "",
          "original_mutation": ""
        },
        {
          "type": "who_confidence",
          "drug": "pretomanid",
          "confidence": "Uncertain significance",
          "comment": "Not found in WHO catalogue",
          "source": "",
          "original_mutation": ""
        }
      ],
      "consequences": [
        {
          "gene_id": "Rv0407",
          "gene_name": "fgd1",
          "feature_id": "CCP43138",
          "type": "upstream_gene_variant",
          "nucleotide_change": "c.-128T>C",
          "protein_change": "",
          "sequence_hgvs": "Chromosome:g.490655T>C",
          "annotation": []
        }
      ],
      "locus_tag": "Rv0407",
      "gene_associated_drugs": [
        "clofazimine",
        "delamanid",
        "pretomanid"
      ]
    },

The "comment" value in the variant["annotation"] element will be set to "Not found in WHO catalogue" if this rule has been applied.