search

iqbal-lab-org / pling

Plasmid analysis using rearrangement distances
MIT License
25 stars 1 forks source link

Plasnet integration PR series (4/5): feat: integrate plasnet into pling #36

Closed leoisl closed 7 months ago

leoisl commented 7 months ago

This is the main PR to integrate plasnet into pling.

Main changes to review:

  1. plasnet works with distances and not similarity. So every reference to jaccard similarity was replaced by jaccard distance (1 - jaccard similarity);
  2. plasnet output files are slightly different from the internal scripts output files, so we have some changes in the rules input/outputs;
  3. This PR also have some small miscellaneous improvements;

There are 3 integration tests that will be PRed after this PR is merged to ensure all these changes are ok.