Allow masking of SNV reference alleles

PlantandFoodResearch / MCHap

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

MIT License

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Allow masking of SNV reference alleles #165

Open timothymillar opened 1 year ago

timothymillar commented 1 year ago

Reusing the REFMASKED flag, allow masking of the reference allele of a SNV in MCHap assemble. This avoids unnecessarily treating a biallelic SNV as triallelic due to the refence genome differing from the population.