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Draft: Fix kmer pangenome structure

Workum, Dirk-Jan van requested to merge fix_kmer_pangenome_structure into develop

The --kmer option with pangenome_structure showed a less smooth curve than the default one with genes; since the code was very old for --kmer specifically, I am refactoring the code first to see if this already solves it. Maybe later we will find the cause and refactor it.

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