predictcoding - multiple mutations at a codon are never evaluated additively

Bioconductor / VariantAnnotation

Annotation of Genetic Variants

https://bioconductor.org/packages/VariantAnnotation

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predictcoding - multiple mutations at a codon are never evaluated additively #46

Open ojcharles opened 3 years ago

ojcharles commented 3 years ago

I have HIV sequence data, where for three consecutive positions I have SNPS. These three all code for SNPS in the same codon. predictcoding() returns the independently evaluated REFAA and VARAA, fine its expected behaviour. But a warning that "hey these variant amino acid mutations aren't true" would be nice!

vjcitn commented 2 years ago

Sorry for delay in answering this. I think it would be great if you would provide a patch/pull request to address this request. Thanks!