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Make the mapper more opinionated about alignment uncertainty #85
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app: backendTask implementation touches the backendTask implementation touches the backendapp: databaseTask implementation requires database changesTask implementation requires database changesapp: frontendTask implementation touches the frontendTask implementation touches the frontendapp: mapperTask implementation touches the mapperTask implementation touches the mappertype: enhancementNew feature or requestNew feature or requesttype: maintenanceMaintaining this projectMaintaining this project
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app: backendTask implementation touches the backendTask implementation touches the backendapp: databaseTask implementation requires database changesTask implementation requires database changesapp: frontendTask implementation touches the frontendTask implementation touches the frontendapp: mapperTask implementation touches the mapperTask implementation touches the mappertype: enhancementNew feature or requestNew feature or requesttype: maintenanceMaintaining this projectMaintaining this project
The mapper currently produces binary mapped/failed outcomes with no confidence gradient. This obscures cases where a mapping succeeded but rests on shaky ground — mismatches, gap-adjacent positions, or ambiguous alignment candidates. A concrete failure case in KSR1 (see thread: https://brotmanbaty.slack.com/archives/C03EN6LRP2Q/p1775772034851719) illustrates how a mismatch-adjacent gap placement led to a silent miscall and pushed a variant into unmapped territory with no indication anything had gone wrong.
The goal of this issue and the subtasks it organizes is to make the mapper fail gracefully and informatively rather than silently, so that downstream users and curators can triage mapping quality rather than treating all outputs as equally trustworthy.