empty results from odgi position

[adadiehl]

Greetings,

I have been attempting to use odgi position to translate coordinates within various assemblies within a minigraph-cactus graph created in-house from 47 HPRC samples and a handful of additional genomes, for 53 phased genomes total, with T2T-CHM13 as reference. I also have coordinates for various features of interest within each of the 53 genomes, in the coordinate frame of the phased genome. I have been trying to use odgi position to translate assembly-specific coordinates to corresponding positions in T2T-CHM13, but for most of these, odgi position returns no output, either to stdout or stderr -- no headers, no nothing, just a command-prompt. For example:

$ odgi position -i chr13.full.og -r T2T-CHM13#0#chr1 3-p HG003#0#chr13#0,117571125
$

All of these features are expected to be physically absent from the reference, so they should exist as bubbles (or parts of nested bubbles) in the graph. I would expect that the returned position would be the start position of the bubble in T2T-CHM13, and in some cases this is true. I have verified this with odgi extract and odgi viz to visualize the regions of interest. However, I am unclear on what it means when nothing is returned. How am I to interpret such results?

Best,
Adam