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vgteam / sequenceTubeMap

displays multiple genomic sequences in the form of a tube map
MIT License
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Alignments still loop around #360

Closed adamnovak closed 9 months ago

adamnovak commented 10 months ago

The NYGC folks say that alignments produced by current versions of Giraffe are still looping around when viewed on the tube map. They're going to provide files to align with Giraffe to replicate the issue, and we're going to fix it properly.

adamnovak commented 10 months ago

I think this may be a symptom of using the wrong graph to construct the premade chunk for the tube map. If the reads are aligned to a Giraffe GBZ, you need to use that graph as the graph for preparing the chunk. You can't use the original GFA used to build the GBZ, if the GFA and GBZ do not actually share a consistent node ID space. You can dump all the nodes in a pair of graphs with something like:

vg view -j whatever.gbz  | jq -c '.node[]'

vg view -j whatever.gfa  | jq -c '.node[]'

If those look different (beyond ordering), the graphs have different node ID spaces.