Replace `--skip-rare-haplotypes` with a generic `--filter-haplotypes` argument.

PlantandFoodResearch / MCHap

Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.

MIT License

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Replace `--skip-rare-haplotypes` with a generic `--filter-haplotypes` argument. #168

Closed timothymillar closed 10 months ago

timothymillar commented 10 months ago

Related to #161 but focusing on filtering input haplotypes.

This would take a generic field of length R or A and a simple comparison e.g. AC >= 1 (three arguments). Any alleles failing the comparison would be excluded (hard-filtered) from the Locus object.

timothymillar commented 10 months ago

Use --filter-input-haplotypes for clarity

timothymillar commented 10 months ago

Fixed in #169