Make WFAExtender apply full length bonuses even though it doesn't use them internally

vgteam / vg

tools for working with genome variation graphs

https://biostars.org/tag/vg/

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Make WFAExtender apply full length bonuses even though it doesn't use them internally #4285

Closed adamnovak closed 1 month ago

adamnovak commented 1 month ago

Changelog Entry

To be copied to the draft changelog by merger:

WFAExtender alignments are now scored using the full length bonus

Description

This makes sure to apply the full length bonus to the scoring of WFAExtender alignments. It doesn't take it into account when choosing the actual alignment path yet, though.