search

waveygang / wfmash

base-accurate DNA sequence alignments using WFA and mashmap3
MIT License
174 stars 18 forks source link

Inversion patching #255

Closed ekg closed 3 months ago

ekg commented 3 months ago

This adds a way to patch in the reverse complement direction when the forward patching fails. It turns this happen. It actually is capable of detecting inversions in the wflign phase, and these can be as short as detectable with this approach.

ekg commented 3 months ago

image

image

ekg commented 3 months ago

This could be improved by recording the successful inverse patches and re-patching around them. It doesn't work exactly this way now.

ekg commented 3 months ago

In any case, the current setup should avoid the forced forward patches that lead to huge numbers of FP variants.