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human-pangenomics / hpp_pangenome_resources

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Notification re: new path names #18

Closed JosephLalli closed 1 year ago

JosephLalli commented 1 year ago

Are the v1.1 graphs supposed to have new names for the reference paths?

In the past I was surjecting into reference paths (aka GRCh38 and CHM13v2 named ${reference}.{contig}, but the Right now I can't surject to the old path "CHM13v2.chr20", for example. The new path name is "CHM13#0#chr20".

While that is probably as it should be,* you might want to let users know about the change.

-Joe

*I get it, adding the #0# specifies the reference allele and brings the reference path names up to the same spec as the rest of the paths, thus allowing for better tool interoperability.

glennhickey commented 1 year ago

Yeah, the name change of the vg paths is necessary to be compatible with current versions of vg. I've added a note in #19 -- thanks for bringing this up.