Version 1.2.2

Version 1.2.2 - 2023-03-29

• Repair the pipeline module.

Version 1.2.1

Version 1.2.1 - 2023-03-29

• Make scaffolding optional in pipeline.
• Remove the option to start with network file.
• Allow parallel scaffolding at the end of the pipeline.
• Force pairix index used in the contact map module.
• Change pairs from option to arguments to handle easier multiple files as
  arguments.
• Debug scaffold module default parameters.
• Update docs.

Version 1.2.0

Version 1.2.0 2023-03-17

• Remove the skip validation option.
• Use miComplete instead of checkM for the recursive step.
• Make multiple recursive step if necessary.
• Sort pairs and do the scaffolding in the pipeline module.
• Add QC, pairs and scaffold modules.
• Correct pairs indexed loading.
• Add option to remove reads mapping at the edges of the contigs.
• Add possibility to used compressed pairs as input.
• Parallelization of the recursive step.
• Change bin id to make them sortable.
• Correct reads extraction bugs for contact map module.
• Correct bugs from cutsite mapping mode.
• Remove Looseversion sorting Warning.
• Update requirements file.
• Change output plot colors.
• Add tests for QC module.
• Update tests of network, partition and validation modules.
• Update documentation.

Version 1.1.6

Version 1.1.6 - 2022-10-06

• Add iterative and cutsite alignment mode.

Version 1.1.5

Version 1.1.5 - 2022-07-05

• 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.

Version 1.1.4b

Correct broken release 1.1.3

Version 1.1.4

Correct type issue in figures modules.

Version 1.1.3

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

Version 1.1.2

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

Version 1.1.1

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.