fix: clarify which-arg accepted types (#34) and ... argument docs (#31)#108
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fix: clarify which-arg accepted types (#34) and ... argument docs (#31)#108jmg421 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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Issues fixed
#34 — ScanVcfParam
whichparameter description inconsistencyThe
\item{which}description inman/ScanVcfParam-class.Rdonly mentionedGRanges, but the constructor (which delegates toRsamtools::ScanBcfParam) also acceptsGRangesListandIntegerRangesList. Updated:\item{which}argument entry to list all three accepted types and add a note that range-based subsetting requires an index file.#31 — Ambiguous description of
...for readVcfThe single
\item{\dots}entry said only "Forimport, the arguments are passed toreadVcf", leaving the behaviour forreadVcf,readInfo,readGeno, andreadGTundocumented. Replaced with an\itemizeblock that calls out each function's...routing explicitly.Changes
man/ScanVcfParam-class.Rd— expandedwhichdescription; fixed constructor noteman/readVcf-methods.Rd— expanded...description with per-function routingCloses #31
Closes #34