docs: clarify REFCODON/VARCODON use transcript-strand coordinates (#43)#105
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jmg421 wants to merge 3 commits into
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docs: clarify REFCODON/VARCODON use transcript-strand coordinates (#43)#105jmg421 wants to merge 3 commits into
jmg421 wants to merge 3 commits into
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Convert \itemize blocks that used \item{label}{desc} syntax to \describe,
and replace empty \item{}{} labels in \describe blocks with the function
signature from the body, resolving all checkRd warnings in isSNV-methods,
PolyPhenDb-class, readVcf-methods, SIFTDb-class, summarizeVariants-methods,
VariantType-class, VCF-class, VcfFile-class, VCFHeader-class, VRanges-class,
and VRangesList-class Rd files.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Fixes #43
Problem
Users reported that
REFCODONdoesn't match the VCFREFfield for minus-strand genes. This is actually correct behavior — codons must be in transcript orientation for valid translation — but the documentation gave no hint of this.Fix
Expanded the
REFCODONandVARCODONsections inpredictCoding-methods.Rdto explicitly state:No code changes — the existing logic is correct.