fix: honour .vcf.gz suffix in writeVcf(index=TRUE) (#35)#109
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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(vcf, "out.vcf.gz", index=TRUE)silently renamed the output toout.vcf.bgzbecauseRsamtools::bgzip()always writes to<stem>.bgz. This broke interoperability with tools (IGV, bcftools, etc.) that expect.vcf.gz.Fix
After
bgzip()+indexTabix(), if the originalfilenameended with.gzand the bgzip'd path differs from it, we rename both the compressed file and its.tbiindex to the user-requested paths. The.bgzdefault behaviour is preserved when the filename does not end in.gz.Behaviour after fix
out.vcfout.vcf.bgz(unchanged)out.vcf.bgzout.vcf.bgz(unchanged)out.vcf.gzout.vcf.gz✅Changes
R/methods-writeVcf.R— capture desired path beforebgzip(); rename if neededman/writeVcf-methods.Rd— document the.gzbehaviour in theindexargument entryCloses #35