neherlab / pangraph

A bioinformatic toolkit to align genome assemblies into pangenome graphs
https://neherlab.github.io/pangraph
MIT License
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fix: apply deletions without causing frame shifts #71

Closed ivan-aksamentov closed 4 months ago

ivan-aksamentov commented 4 months ago

Instead of stripping deleted ranges wight away, I first replace these ranges with character -. At the end of the function I strip all characters -.

This is to ensure that no reading frame shifts introduced and that all deletions and insertions are applied to correct positions.