Align target sequence to selected transcript at the protein level

[bencap]

When mapping protein-level variants, the mapper currently assumes the target sequence aligns to the reference starting at a fixed offset with no gaps. This produces incorrect mappings when the target protein doesn't align cleanly to the reference — for example, when there are internal gaps or the target covers a non-contiguous region of the reference.

This change should introduce a protein-to-protein alignment step (via BLAT) between the target sequence and the selected transcript's reference protein. Variant positions will then be mapped through the actual alignment subranges rather than a simple offset, correctly handling gaps and partial coverage.

Motivation:
Improves accuracy of protein variant coordinate mapping for targets whose relationship to the reference protein is more complex than a simple positional shift.