Computes a quantitative measure that assesses accuracy of network inference by also accounting for indirect paths

[adbharadwaj]

• Added option to compute $k$-P-R curves defined as follows: a predicted edge $(a,b)$ is a TP if there is a path of length $\leq k$ between $a$ and $b$. So a $1$-P-R curve is just the regular P-R curve.
• Added option to specify reference network file as command line option. This option can be used to evaluate GRNs from real data on STRING interactions.
• Added option to specify if the predictions and reference network should be treated as undirected. This option can be used to evaluate GRNs from real data on STRING interactions since STRING interactions are undirected in nature.