The mapper returns the top-scoring alignment without indicating whether the decision was clear or marginal. When the score delta between the top two candidates falls below a configurable threshold, record an ambiguity flag on the mapping record rather than silently returning the winner. Store the score delta and, when flagged, the alternative alignment. In KSR1, coincidental identity at SA (506-507) made an incorrect gap placement locally competitive — a score delta flag would have surfaced this ambiguous alignment.
The mapper returns the top-scoring alignment without indicating whether the decision was clear or marginal. When the score delta between the top two candidates falls below a configurable threshold, record an ambiguity flag on the mapping record rather than silently returning the winner. Store the score delta and, when flagged, the alternative alignment. In KSR1, coincidental identity at SA (506-507) made an incorrect gap placement locally competitive — a score delta flag would have surfaced this ambiguous alignment.