fix: writeVcf.VRanges forwards info/filter/meta args to asVCF (#61)#110
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fix: writeVcf.VRanges forwards info/filter/meta args to asVCF (#61)#110jmg421 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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Problem
writeVcf(VRanges, ...)was implemented as:The
as(obj, "VCF")coercion ignores all extramcols()columns as INFO fields — it always treats them as FORMAT/genotype fields. This meant there was no way to write aVRangesto VCF with INFO fields, even thoughasVCF(vr, info="COL")already supports this.Fix
Changed
writeVcf.VRangesto callasVCF(obj, info=info, filter=filter, meta=meta)instead ofas(obj, "VCF"), and exposedinfo,filter, andmetaas explicit arguments (mirroring theasVCFsignature).Changes
R/methods-writeVcf.R: new signature forwriteVcf,VRangesmethodman/writeVcf-methods.Rd: document VRanges method and newinfo/filter/metaargs; add aliasAll existing
writeVcfunit tests pass. Backward compatible — callingwriteVcf(vr, file)withoutinfoproduces identical output to before.Closes #61