Metator

- Add possibility to start with bam files.
- Add SCN normalization to balance the heatmap.
- Add conda environnement and docs.
- Add prefix name for metator contact map.

- Avoid raising error if no pairs extracted in contact map module.
- Add network heatmap plot in the ouput.

- Add the possibility to read pairix index files in the contact map module to retrieve faster pairs from a 2D region.

Correct some minor issues:

- Correct pairs files:
- Correct position index (previously 0-based but should be 1-based).
- Change pairs entry to have an upper triangle shape.
- Correct recursive bin issue in the contig data file were unbinned contigs or binned contigs in bins smaller than the size threshold given were given an id of an existing bin.
- Correct issue in the contact map were contigs needed to be size sorted if a size threshold were given.
- Add some multiple network files in the output if multiple input samples were given.

- Add some Figures in the output:
- Completion/contamination distribution of the MAGs.
- Distribution of the quality of the MAGs in the assembly.
- Distribution of the GC and coverage inside each MAG.
- Add test for the new figure module.
- Add a module contactmap to build HiC matrix from some metaTOR objects such as contigs, bins, or other objects with contigs labels from the user. It could be use with metator contactmap [arguments]. The output could be use then with hicstuff view or cooler show to visualize matrix or with instagraal to try to scaffold MAGs.
- Modify the pairs files:
- Change pairs file extension to .pairs.
- Reorder the columns of .pairs file: readID-chr1-pos1-chr2-pos2-strand1-strand2 instead of readID-chr1-pos1-strand1-chr2-pos2-strand2.
- Use tabulation to separate column instead of space to match the official specification.
- Correction of some minor issues:
- Stop the duplication of the logging message.
-Silence the HTSlib index error (from pysam.AlignementFile) which was meaningless.
- Remove pyfastx index.
- Put as optional the output of the clustering matrix which needs high memory usage for large assembly and optimize memory usage to build it.
- Modify Assignment method to dataframe to avoid assignment to copy of the dataframe (SettingWithCopyWarning).