Many scaffold sequences are hard coded

[cnobles]

Sequences that appear outside of the linker or primer region are hard coded. Best if these could be arguments to give so the utility could be applied to other sequencing methods. Also no diagram is given for how each of these sequences are pieced together.

[aubreybailey]

Cant speak to the first point, but if you're having trouble with visualization of read-pairs, I recommend IGV, CLC, or Geneious. You'll be -much- happier than trying to do it in R