Fix incorrect alignments in Giraffe when a tail doubles back onto the anchor node #4534
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…ck around to the cut node for the right anchor
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Changelog Entry
To be copied to the draft changelog by merger:
vg giraffeshould no longer produce final mappings with nonzero offsets or other wrong answers when a read tail doubles back on itself.Description
This should fix the problem Zilan reported where a read couldn't be converted to GAF, because it had an offset on its last mapping, because when the flipped right tail was aligned right-anchored it doubled back onto the anchoring node and the extra cut-off part wasn't accounted for when translating back to the base graph.
I'm also adding more asserts, because we wouldn't have ever noticed this in GAM output mode, only GAF.