small fix im "mapping reads to contigs"- script
Small fixes:
 1 output 'n' instead of 'N' in case of inferred gap of <= 1bp
 2 specify -g  (flag) instead of -g 1 as argument to besst (-g still under development)
 3 Statistics file now outputs which paths that were taken out of the ones printed to the file
 4 Fixed bug of number of cores used for BWA in mapping script
Started working on module for more accurate gap size calculations when contigs
are small compared to library stddev and we have links between several contigs in
a cluster. We can then get a compound likelihood from all the observations.
Added improved gap estimation for paths with lots of small contigs.
Both between and within scaffolds
Finished implementation of gap estimations for fragmented paths
removed print statement in MakeScaffolds
Fixed bugs in pathgaps.py. Implemented two different methods for searching for ML gaps in paths (MCMC and ordered search). Ordered search is faster but more greedy. It seems to perform well on average though.
removed print statement
Added LP solver for pathgaps.py
Gaps in paths are no estimated with a GapEst+LP technique that minimizes an objective
of expected gap differences between GapEst estimates and the cuttent value of the gap values.
We use Simplex method for the LP.
added parameter --separate_repeats. Updated Versions.txt (durrent version is to be relaesed as v1.1)
changed output of Within scaffolds in ELS. Commented out print statements.
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
Changed constraint boundaries for gap variables. Changed lower score threshold in pathfinder to 1.
removed constraints on insert size in LP program. Works better since parameter space is bigger.
Updated objective function in LP to weight for contamination ratio
Added comtamination ratio to parameters and now, LP is forbidding PE oriented onservations larger than mean + 6*stddev