surject: rank paths by their best alignment - #5009
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Changelog Entry
vg surject -mnow ranks each target path using its bestnon-supplementary surjection.
Description
When multiple non-supplementary surjections were produced for one path,
path ranking used the first one encountered. This could select a lower-scoring
alignment and rank the path incorrectly.
This change examines every non-supplementary surjection and uses the highest
score for each path. Paths containing only supplementary alignments retain
a score of zero.
The behavior is updated for both Alignment and MultipathAlignment input.