Handle graphs with overlap?

[dirkjanvw]

Hi! Seeing the paper of your tool, it sparked my interest to compare some GFA files of alignment-based tools (like minigraph-cactus) to de bruijn graph-based tools (like cuttlefish). I tried to run it, but I am facing two issues:

1. [minor] It seems rs-pancat-compare assumes a certain order in the GFA file: first H-line, then S-line, then L-line and lastly P-line. This is not always the case for GFA files, though. I can fix this myself by reordering the lines, but ideally I shouldn't have to do that (or have some easy to understand error message).
2. [major] It seems rs-pancat-compare doesn't handle overlapping nodes where the overlap is specified in a CIGAR string in the L-line. In de Bruijn graphs, these are typically always k - 1 long (e.g. 26M when k = 27). It gives errors such as: # Error: the two paths representing NC_001136.10 have different lengths: 3399825 and 1531933. whereas the underlying sequence is identical in length for sure.

Perhaps if you continue to improve rs-pancat-compare, these two would be nice features to add :)

[dubssieg]

Hello ! Thank you for your interest in our tool.

1. I've updated the code to support any order of lines in the input file. There is a slight tradeoff between memory and time (slightly longer on large files, but a little less memory-consuming) with the introduction of this modification (see #031c165).
2. As originally imagined and presented in the publication, the implementation does not support the presence of overlaps. This could be an interesting avenue to explore, but would require substantial revisions to the code. I'm thinking about how best to integrate this as I continue development. For the moment, I think the simplest way is to compact the dBG strings and compare two sequence graphs.

I'll update the issue as I develop further in this direction. Have a nice day!

[dubssieg]

As far as I know, there's two already existing tools that can acheve what you are after: GetBlunted (vgteam) and stark (hnikaein). Maybe it could help a little?

Have a nice day!