bug report: junction extract tool should not count overlapping reads as double support for a junction #187
Description
In the current implementation, read-mates can provide 2 "counts" to the same junction if they both span it. This results in inflated counts and therefore inflated significance when downstream tools consider the counts.
I would like to advocate for each queryname to be able to provide a maximum of 1 count towards any single junction. This must be implemented carefully so memory use doesn't spike too much.