Added calculation of MP library contamin ratio and the contamine read distribution (rc oriented).
This version is also using mathstats 0.1.2  (better lower boundary for search of ML gap size) instead of v0.1
Implemented ILP for finding best path given MP contamination with PE oriented reads.
Finalized implementation of LP for ordering contigs in gaps.
Merge branch 'feature/frag_orient_contamination' into develop

formation to get more accurate order and distance of contigs
Merge branch 'feature/frag_orient_contamination' into develop