relax gaf/paf filtering on first stage of mgSplit pipeline#1942
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@Sagorikanag found a bug where
chrYwould get dropped when runningcactus-pagnenome --mgSpliton a 3-genome graph. The root issue seems to be that the--mgSplitworkflow first builds a reference only graph (just CHM13 in this case), then runs the usual splitting pipeline on that. But this also triggers a bunch of the gaf/paf filtering that normally happens in this stage. In particular, the paf overlap filter gobbles up the linear chrY alignment because of large ambiguous blocks.This patch just turns off all these filters for the reference-only graph stages of
--mgSplit.By virtue of having 2 references (CHM13 and GRCh38), the v2.1 HPRC graphs seem to avoid this issue (and probably why I never ran into it). But I think it's a pretty serious once that could cause contigs to be dropped by
--mgSplitwith a single--referencein many cases...