fix: transparently handle regular-gzip (bcftools -O z) VCFs (#32)#107
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fix: transparently handle regular-gzip (bcftools -O z) VCFs (#32)#107jmg421 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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…ioconductor#32) .is_bgzf() detects BGZF vs regular gzip via the 'BC' sub-field magic bytes in the gzip extra header (bytes 13-14 = 0x42 0x43). .ensure_bgzf() is called from .checkFile() (readVcf) and the scanVcfHeader character method: if a .gz file is not BGZF it is transparently re-compressed to a BGZF tempfile so that scanBcfHeader / htslib no longer throws '[internal] _hts_rewind() failed'. Adds test_regular_gzip_readVcf() regression test.
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Superseded by #112, which adds proper tmpfile cleanup via |
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Problem
Files compressed with
bcftools view -O z(or plaingzip) produce regular gzip, not BGZF. htslib'sscanBcfHeaderrequires BGZF and throws[internal] _hts_rewind() failedwhen given a regular gzip file, makingreadVcfandscanVcfHeaderunusable on such files.Fix
Two new internal helpers in
R/methods-readVcf.R:.is_bgzf(path)— inspects the gzip extra-field sub-field magic bytes (0x42 0x43= 'BC' at bytes 13–14) to distinguish BGZF from regular gzip..ensure_bgzf(path)— if a.gzfile is not BGZF, transparently re-compresses it to a BGZF tempfile usingRsamtools::bgzip()and returns the temp path..ensure_bgzf()is called from:.checkFile()(used byreadVcf) before theTabixFile()callscanVcfHeader("character")method beforescanBcfHeader()A message is emitted so users know re-compression occurred.
Tests
Added
test_regular_gzip_readVcf()ininst/unitTests/test_readVcf-methods.Rwhich:.is_bgzf()returnsFALSEfor it andTRUEfor the original BGZF filereadVcf()succeeds and returns a non-emptyCollapsedVCFAll existing
test_readVcf-methods.Rtests continue to pass.Closes #32