Fix for circular references

[lcoombe]

• 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