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iqbal-lab-org / pling

Plasmid analysis using rearrangement distances
MIT License
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length_threshold is not used at all in seq_jaccard.py #30

Closed leoisl closed 7 months ago

leoisl commented 8 months ago

length_threshold is declared as a parameter in the rule that calls seq_jaccard.py: https://github.com/iqbal-lab-org/pling/blob/87e571ecb5cc6b7743471515d65f7a1a5355695e/pling/jac_network_snakemake/Snakefile#L54

and is declared as a parameter in the function to get the sequence jaccard: https://github.com/iqbal-lab-org/pling/blob/87e571ecb5cc6b7743471515d65f7a1a5355695e/pling/jac_network_snakemake/seq_jaccard.py#L21

but it is not used at all in this function to compute the gene jaccard. I am assuming this is just an extra unused parameter and will refactor by removing it from the rule and the function, but let me know if actually this is a bug and the length threshold should be considered when computing sequence jaccard.

babayagaofficial commented 7 months ago

nope it's not used, feel free to refactor!