Version 1.1.0

• 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).

Version 1.0.4

• 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.

Version 1.0.3

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

Version 1.0.2

• 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.

Version 1.0.1

Correct bug in validation module:

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

Version 1.0.0

New version of metaTOR in Python3