Counterintuitive/wrong? offset from genomic to transcript mapping

[jsstevenson]

Describe the bug

Mapping the beginning genomic coordinate of exon 1 on ELN on a GRCh37 accession produces a genomic data description with an exon offset of -97. This is counterintuitive (wrong even?) -- I would expect it to map to the beginning of exon 1 on a GRCh38 accession, ie it should map to exon 1 with offset 0.

Steps to reproduce

from cool_seq_tool.app import CoolSeqTool
import asyncio

from cool_seq_tool.schemas import Strand

async def do_thing():
    cst = CoolSeqTool()
    result = await cst.ex_g_coords_mapper.genomic_to_transcript_exon_coordinates(
        alt_ac="NC_000007.13",
        start=73442503,  # this is the start of exon 1 on this gene/ac -- see https://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_000007.13&tkey=KAJKLycgLCUiKyYpDRw5JR9XRUpiWVlhdUpVf1zLfSA0VyXsgas3w_8zqs-w-8PLsK8&assm_context=GCF_000001405.25&app_context=gene&v=73442488:73442615&c=null&select=null&slim=0
        strand=Strand.POSITIVE,
        gene="ELN",
    )
    print(result.genomic_data.exon_start_offset)

asyncio.run(do_thing())
# -97

Expected behavior

Should be an exon offset of ~0

Current behavior

Gives an offset of -97

Possible reason(s)

_set_exon_offset looks fishy imho

Suggested fix

No response

Branch, commit, and/or version

efa56e1

Screenshots

No response

Environment details

mac

Additional details

I have yet to find another example of a gene on GRCh37 that maps to a transcript at all, so this might be specific to this gene

Contribution

Yes, I can create a PR for this fix.

[korikuzma]

@jsstevenson by the way, I am making quite a few changes in the mapper class. So not sure if you want to tackle this or I can.

[korikuzma]

@jarbesfeld says this expected output from #352 is correct:

{
  "gene": "ELN",
  "genomic_ac": "NC_000007.14",
  "tx_ac": "NM_000501.4",
  "seg_start": {
    "exon_ord": 0,
    "offset": 1,
    "genomic_location": {
      "type": "SequenceLocation",
      "sequenceReference": {
        "type": "SequenceReference",
        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
      },
      "start": 74028173
    }
  }
}

[korikuzma]

This was completed in #352