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is there a way to extract from a graph with uncompacted node IDs? #497

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esrice opened this issue Apr 18, 2023 · 0 comments
Open

is there a way to extract from a graph with uncompacted node IDs? #497

esrice opened this issue Apr 18, 2023 · 0 comments

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@esrice
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esrice commented Apr 18, 2023

I'm trying to extract a subgraph like so:

odgi extract -d100 -r'genome1#chr1:11159196-11400464' -o out.og -i pangenome.og

but receive the error

[odgi::extract] error: the node IDs are not compacted. Please run 'odgi sort' using -O, --optimize to optimize the graph

However, when I use the optimized graph, it of course has different node IDs than the original input gfa. This is a problem as I have a vcf containing node IDs from the unoptimized graph, and I want to be able to cross-reference between the subgraph and the vcf. Is there any way to do this? Thanks!

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