Found bug where nucmer was reporting a single match without indels as two matches with disparate lengths, which broke coordinate projection and made the overlap splitting get stuck. Switched from using dnadiff to nucmer with suitable parameters, which appears to have fixed all issues.
Found bug where nucmer was reporting a single match without indels as two matches with disparate lengths, which broke coordinate projection and made the overlap splitting get stuck. Switched from using dnadiff to nucmer with suitable parameters, which appears to have fixed all issues.