Initial version of linkage information table generator. Too slow atm, takes about 9m on 100 reads test data. Needs more testing to validate results, but first tests seem ok.
Changes column order
Merge branch 'master' of github.com:BinPro/CONCOCT
Added -m help in the readme
Reads bam file in one go, instead of fetching each contig separately. Takes about 5 min now for 100 reads instead of 10m. Have to see how time increases with larger data set.
Fix region length bug. Change region length parameter to integer.
Fix error in linkage dict creation
Change gen_input_table to reuse bed histogram files, instead of recomputing them.
Add linkage test data
Merge branch 'master' of https://github.com/BinPro/CONCOCT
Adds multiprocessing for parsing multiple bam files in parallel.
Adds validation script that uses Melanie's read simulation.

The reads Melanie simulated have the name of the reference they are from in
their name. After mapping the simulated reads, one can therefore determine
where each read is stemming from. This script outputs a table where each row
has the counts per genome for a contig, which can be useful for validation.
CONCONCT needs python version 2.7
Moved the output class to the output module