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iqbal-lab-org / pandora

Pan-genome inference and genotyping with long noisy or short accurate reads
MIT License
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feat: adds parameter --min-gene-coverage-proportion to pandora map, compare and discover #351

Closed leoisl closed 7 months ago

leoisl commented 7 months ago

This PR adds the parameter --min-gene-coverage-proportion to pandora map, compare and discover subcommands:

  --min-gene-coverage-proportion FLOAT
                              Minimum gene coverage proportion to keep a gene. Given the coverage on the kmers of the maximum likelihood path of a gene, we compute the number of bases that have at least one read covering it. If the proportion of such bases is larger than the value in this parameter, the gene is kept. Otherwise, the gene is filtered out. [default: 0.8]