Hello, I am mapping a diploid phased assembly on an haploid reference. I would like a tool that naively output all character states for each mapped position. Exactly like you would if you were to record by hands the character states for each position you look at. Bcftools mpileup doesn't work well for that because it outputs likelihood calculation and wild card allele. I don't need that. Any idea? Or it will be a custom htslib exe?

Thanks a lot