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Hi,

I was running into an issue with clusty when I was giving it a file ANI file with only a single vertice & an edge to itself.
For example:

name1	name2	id1	id2	ani
xxx	xxx	10	11	0.93

Originally, one would get the following error:

Clusty
  version 1.2.2-b687638 (2025-05-22)

Loading pairwise distances from synth.singleton.ani ... 
  input graph: 0 nodes, 1 edges
  filtered graph: 0 nodes, 0 edges
  time [s]: 0.0316375
Saving clusters (representatives = true)... 
 41 Segmentation fault      (core dumped)

I was wondering if it would be possible to implement the following fix:

  • Allow self edges in parseBlock
  • Remove self edges in updateMatrix
  • Writing output file with only singletons in main.cpp

Sorry if the PR looks messy, my linter deleted a bunch of unnecessary spaces. I can reinclude the spaces if you want to make the diff easier.

@Joon-Klaps Joon-Klaps changed the title Bugfix: Allow a singleton with self connection as input Bugfix: Allow a singleton with self edge as input Dec 19, 2025
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