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Draft: Removing genomes from an existing pangenome.

Lankveld, Thijs van requested to merge remove_genomes into develop

Debugging still in progress.

Tested on chloroplasts datasets: add C_sativus then Z_mays; then remove Z_mays.

Currently export comparison:

  • anchors: correct
  • nodes: correct except pangenome node: a few properties are not correctly updated; num kmers will be an issue, because kmers of Z_mays get node index -1L, instead of being removed from the index database (maybe keep track of kmers that would have been removed and reduce pangenome property by that).
  • relationships: incorrect: seems to be a repetition problem where all positions on the remaining genome are put in there publicate (maybe only for some edges).


  • test on more chloroplasts, also testing removing genome other than last one.
  • test on hiv datasets (Sandra).
  • discuss future steps for handling removed genomes and the 'empty space' they leave in some listed (array) properties.

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