How to use Codfreq for the other subtypes?

[gpcr]

KU820846.CRF08_BC.json

How to use Codfreq for the other subtypes?
Also trying to understand gene annotations and relGapPlacementScore used for each

For example Subtype A1 (KX232620) directly instead of HIV1 (B)

I parsed the genbank file (KU820846) to json file (attached) similar to HIV1.json format, but not clear with PR, IN, RT coordinates to use for various subtypes including hybrids, insertions and deletions scores
Any help deeply appreciated:

{
      "fragmentName": "pol",
      "fromFragment": "HXB2_x_ConsensusB",
      "geneName": "pol",
      "refRanges": [[2088, 5093]],
      "codonAlignment": [
        {
          "minGapDistance": 15,
          **"relGapPlacementScore": "669/3ins:20,669/6ins:30,669/9ins:40,669/12ins:50,2907/6ins:20"**
        }
      ]
    },
    {
      "fragmentName": "PR",
      "fromFragment": "HXB2_x_ConsensusB",
      "geneName": "PR",
      "refRanges": [[2253, 2549]],
      "codonAlignment": [
        {
          "minGapDistance": 15
        }
      ]
    },

[philiptzou]

Hi @gpcr, the numbers are NA positions (starting from 1) in the reference sequence. In addition, the ranges are inclusive on both side.

See the type definition: https://github.com/hivdb/codfreq/blob/main/codfreq/codfreq_types.py