Metator

- Change the format of the pairs file to match with the official specification.
- Add the HiC coverage (mean number of contacts in 1kb region) in the final bin summary.
- Add possibility to start with the pairs file.
- Add info about general alignment if multiples files are given.
- Organize temporary folder.

- Add clustering matrix in the output of the partition, validation and pipeline modules.
- Add output files documentation.
- Add codeco.

- Modification of the ouput files:
- Add bin coverage based on the depth file given in the bin_summary file.
- Add a final bin column in the contig data file after the validation to specify the name of the final bin of the contig. A "ND" value is given if the contig isn't binned.
- Add the pairs file of the alignment to be able to produce HiC matrices from it using hicstuff for example.
- Add a log file with all information of the run.
- With the pipeline workflow remove intermediate contig data files.
- Modify call to input data to use only header names and not order of the column.
- Change the parameter of the bowtie2 alignement back to --very-sensitive-local.
- Add the total size of the different category of bins in the log.
- Correct minor issues in the doc.

Correct bug in validation module:

- louvain_recursif: correct type error to identify contigs of a subnetwork which could triggers empty subnetwork error.

New version of metaTOR in Python3