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vgteam / sequenceTubeMap

displays multiple genomic sequences in the form of a tube map
MIT License
180 stars 25 forks source link

Support BED in full coords, premade chunks, and setting right offset from path name in [] #326

Closed adamnovak closed 1 year ago

adamnovak commented 1 year ago

The Lancet folks want to be able to have their small chunks from the BED file display as having the correct positions in the full graph.

We need to make sure that the chunk extraction script properly sets the [] offsets in the reference path names, and that we have documentation about how to do that by hand in a GFA for a chunk (or a vg for a chunk if you have to convert).

We also need to make sure that that offset information is properly picked up and put in the server response so the ruler draws right.

adamnovak commented 1 year ago

It turns out this works differently: vg chunk is asked to write a regions.tsv for each chunk directory, and that holds the start and end coordinates along the path; the chunk is expected to not use the [] syntax.