fix!: Add support for residue coords + refactor offset calculation

[jarbesfeld]

closes #383 and #389

• This PR includes a refactor of the exon offset calculation to make this step more efficient and understandable
• This PR also includes support for residue coordinates. The fusion callers I've been working with output residue-coordinates, so when the offset is computed with respect to alt_start_i, the genomic position must be reduced by 1 as the exon boundaries provided by UTA are inter-residue coordinates. This adjustment is not needed however when the offset is computed using the genomic coordinate in alt_end_i

[korikuzma]

Code seems good to me. Relying on @ahwagner to confirm logic makes sense.

[korikuzma]

Quick initial review. I'm going to have to take more time to review the changes.

[korikuzma]

Small thing