pangenome / odgi

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
https://doi.org/10.1093/bioinformatics/btac308
MIT License
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`odgi inject`: use a key that is really unique across annotations #476

Closed AndreaGuarracino closed 1 year ago

AndreaGuarracino commented 1 year ago

This was leading to invalid paths when there were overlapping annotations to inject. See #475.

AndreaGuarracino commented 1 year ago

Still buggy

cat t.gfa
H   VN:Z:1.0
S   1   ATCG
P   x   1+   *

odgi inject -i t.gfa -b <(echo -e "x\t1\t3\tA\nx\t1\t2\tB") -o - > /dev/null
[odgi::algorithms::inject_ranges] injection end point for interval B is not at a node boundary: off by 2 vs 3 on a node 1bp long
AndreaGuarracino commented 1 year ago

Inverting the end coordinates works:

odgi inject -i t.gfa -b <(echo -e "x\t1\t2\tA\nx\t1\t3\tB") -o - > /dev/null