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To-do

  • Mapping genes to reference sequences
  • Gene density src/pangebin/gene_density/todo.md
  • Seed sequences src/pangebin/seed/todo.md
    • Threshold: Nextflow pipeline
  • GC content src/pangebin/gc_content/todo.md
  • Adapt PlasBin-flow src/pangebin/plasbin/todo.md
  • PangeBin-flow on pansm from PBf inputs
    • Correct the contigs names as in the plasmidness and seed files they are not formatted as in the panassembly graph (from std asm graph)

Working changes

Warning

  • Clean once tmp internal experiments
    • Many things differ between once and decomp and binlab
      • Use same constraint structure as in decomp and binlab
      • Inspire from multi-flow to create a once-2 binning appraoch (hiearchizing the topology and seed constraints)
  • Clean classbin tmp internal experiments

Perspectives

Methods

  • Result filter utilities (on bins...)

Features

  • Verify parameters given in configs (through typer and configs API)

Remarks

  • Minimum flow:
    • to adress non-0 flow issue
    • how to interpret dp? (why so low?)
    • when the MipGap is to high, the total flow always equal to the minimum flow: big loop

From log gurobi:

Warning: Model contains large matrix coefficient range
         Consider reformulating model or setting NumericFocus parameter
         to avoid numerical issues.