How should we interpret SR of the L line in rGFA

[SHuang-Broad]

Hello Heng,

While I'm playing with the example assemblies on the FTP site, I noticed that (all) the L-lines in the rGFA file also have the SR tag, which isn't a required tag according to the rGFA format (only the S-Lines are required to).

So how should we interpret them?

Thanks!
Steve

[lh3]

SR on L-lines plays the same role as SR on S-lines. Think about a deletion from the reference. If you don't keep SR on L-lines/links, you don't know how to traverse the reference path.

[SHuang-Broad]

What about L-lines that connects two segments of different ranks?
Would the L-line take the rank from the segment of higher priority (i.e. lower rank value)?

[lh3]

A link shouldn't have a lower rank than the two segments. Think about the minigraph incremental graph construction procedure. SR on L-line is a natural outcome.

[SHuang-Broad]

Sorry, I meant a link that links together two segments having different ranks,

e.g. a link that links together one segment from GRCh38 and one segment from CHM13 (T2T).

If the rGFA file was built started with GRCh38 (hence rank 0) then with CHM13 (hence rank 1),
then should I expect the link in this example to have rank 0?

[lh3]

Probably not.