Investigate if graph alignments of nanopore reads that get long softclips at surjection are correct

[adamnovak]

Around https://ucsc-gi.slack.com/archives/CJ2EHEH1A/p1721346811431889 Jordan notes that he has some nanopore reads that acquire long softclips when they are surjected. We should see if the graph alignments they started with have something wrong with them to cause this.

[adamnovak]

@jeizenga I think you might have resolved this question of nanopore read softclips at surjection. Do you think we can close this? Or is there a list of reads you still want someone to investigate at the mapping stage?

[jeizenga]

I think we understand what they are now, but I'm not sure we've fully resolved how we want to handle them. The question is how much work to put into realigning to paralogous sequences on the reference.