Spurious breakpoint filtering

[dubssieg]

Following a remark by Adam Novak, I add with the release v0.1.3 support for discarding of spurious breakpoints.

Spurious breakpoints

Spurious breakpoints are a position in between a couple of nodes (x,y) which are contiguous in at least one path.
Formally, deg⁺(x) = deg⁻(y) = 1

Those do not represent a meaningful biological information. They are induced by graph construction process, and does not does not imply existence of the end of an homology block. Moreover, with formats like .gbz, nodes are splitted and this could mitigate the issue.

I added to the command-line a -s flag to tell pancat to filter out such breakpoints.