Fix for circular references #113
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lcoombe
commented
Aug 19, 2024
lcoombe
commented
- I found that in some cases, using a circular reference can lead to no scaffolds being scaffolded
- With some investigation, it was due to the checking for start/end nodes in the linear graph search step
- We relied on looking for nodes with a degree of 1 at either end of the linear segment, but it is possible for a perfect circular path to be a valid graph segment, meaning that all nodes would have a degree of 2
- With this fix, identify these edge cases, and break the graph at the minimizer node with the smallest position in the reference
- This allows scaffolding to take place properly
* If all of the graph nodes have a degree of 2, no source/target nodes will be found, and currently no scaffolds will be assigned * If this is detected, choose a minimizer node (smallest position in highest weight assembly), and make this the 'source' node * Break the graph at incident edge, and continue the path determination
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