A variant that maps cleanly onto a concordant alignment column is fundamentally different from one that sits on a mismatch or near a gap boundary — but currently they look identical in the output. Compute and store per-variant flags on the mapped variant record:
- Whether the variant position falls on a mismatched alignment column (with target and reference residues both recorded)
- Distance in residues to the nearest mismatch in the alignment
- Distance in residues to the nearest gap boundary
- A boolean flag for proximity to gap within a configurable window (e.g. 5 residues)
These flags should be exposed in the API response. The KSR1 case — where VP→DI was silently miscalled because the variant sat on a mismatch adjacent to a misplaced gap — is the motivating example. Depends on the mapping table (#86) being in place first.
A variant that maps cleanly onto a concordant alignment column is fundamentally different from one that sits on a mismatch or near a gap boundary — but currently they look identical in the output. Compute and store per-variant flags on the mapped variant record:
These flags should be exposed in the API response. The KSR1 case — where VP→DI was silently miscalled because the variant sat on a mismatch adjacent to a misplaced gap — is the motivating example. Depends on the mapping table (#86) being in place first.