Add ref-path stubbification option -S to vg clip #4061
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Changelog Entry
To be copied to the draft changelog by merger:
Description
The end of
chr4in a recent 16-drosophila graph is a big tangle, and we get an edge (from another haplotype) coming out the end of it:This has the effect of leaving the graph with only one tip, which in this case causes it to have 4 top level chains. This in turn causes
vg haplotypesto crash (#4060) sincevg haplotypesassumes one top-level chain per component.This PR adds a
-Soption tovg clipthat, for every reference path, makes sure that both of its endpoints are on tips in the graph. When used in conjunction with the usual stub remover (so-Ss), it will make sure there are exactly two tips per reference path per component in the graph.If the graph has overlapping reference paths, then they will be chopped up by eachother, so probably best to avoid using in this case!!