Gene bed and gene info

EDIT:

I think a better way to phrase this:

When a gene_name/symbol from NCBI in the gene info does not belong to the gene bed file (ensembl version outdated so synonyms changed/areas remapped/discovered,etc), a warning is spit out:
https://github.com/ccmbioinfo/MetaFusion/blob/81df5123ffca922f3c35f0639c640c14badde40e/scripts/pygeneann_MetaFusion.py#L1792-L1795

What happens to the gene in this instance? We are seeing a lot of NoHeadGene/truncated annotations. Gene order will probably not change from the caller in these cases... (since score seems to be dependent on the annotation in the gene bed file) Is anything else effected?

Start at scripts/pygeneann_MetaFusion.py lines 1792-1795 and trace what happens when an NCBI gene_name or symbol is absent from the gene bed file. Follow the annotation path for NoHeadGene and truncated annotations, then check whether caller gene order or scoring is affected. Done means documenting the observed behavior and any affected outputs.

Written by the indexing model from the issue text.