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pangenome / odgi

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
https://doi.org/10.1093/bioinformatics/btac308
MIT License
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Odgi viz: visualize haplotypes #575

Closed SimonaSecomandi closed 5 months ago

SimonaSecomandi commented 5 months ago

Hello,

I'm trying to generate an odgi figure for each PGGB chromosome graph.

I would like to merge paths beginning with prefixes in file (odgi viz with -M option). However, The figure doesn't show the two haplotypes of each sample separately, but it merge all the paths together showing only one line per sample. Is there a way to merge paths for hap1 and hap2 of each samples separately?

This is similar to Minigraph-Cactus odgi figures, but I know the difference is that the prefix in MC is different for hap1 and hap2 (you add .1 or .2 to the samples name), while in PGGB the prefix is the same for both.

Many thanks!

ekg commented 5 months ago

I guess you figured out how to do this?