fix: clarify which-arg accepted types (#34) and ... argument docs (#31)#108
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jmg421 wants to merge 8 commits into
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fix: clarify which-arg accepted types (#34) and ... argument docs (#31)#108jmg421 wants to merge 8 commits into
jmg421 wants to merge 8 commits into
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Bioconductor#86) When query has no overlap with the CDS, .localCoordinates() returns a zero-length GRanges. Previously an early return on length(txlocal)==0 caused REFAA and VARAA to be absent from mcols(), returning NULL instead of empty AAStringSet objects. This breaks downstream operations like reverse() and subseq() on the result columns. Fix: - Remove early return so the full mcols-building code runs even when txlocal is empty, naturally producing zero-length AAStringSet columns - Fix GENEID=NA_character_ -> rep(NA_character_, length(txlocal)) so DataFrame() construction works correctly at zero length Test: extend test_predictCoding_empty to assert REFAA and VARAA are AAStringSet with length 0.
…lassification
Multi-nucleotide variants (MNVs/DBS) can produce VARAA strings like 'P*'
or '*W' where %in% '*' fails to match. Switch to grepl('\*', ..., fixed=TRUE)
so any VARAA containing a stop codon is correctly classified as 'nonsense'
rather than 'nonsynonymous'.
Fixes Bioconductor#86. Adds unit test test_predictCoding_nonsense_DBS covering
a DBS that introduces a stop at a codon boundary.
mcols(rdexp) <- NULL unconditionally erased all user-added metadata columns from rowRanges during CollapsedVCF expansion. Fix: compute the set of non-VCF-fixed columns (anything not in REF/ALT/QUAL/ FILTER/paramRangeID) and retain them in the expanded object; the fixed columns are dropped as before since they are rebuilt from fexp. Fixes Bioconductor#85.
… all-NA seqinfo (Bioconductor#78) - .contigsFromSeqinfo() now returns character(0) when all seqlengths and genome are NA, avoiding noisy '##contig=<ID=x>' placeholder lines - .formatHeader() single-value branch no longer overwrites an existing fileDate with today's date; the original value is preserved - META branch likewise only adds fileDate when absent - Add regression test test_predictCoding_exon_intron_boundary (Bioconductor#83)
Bioconductor#80, Bioconductor#89) htslib/scanBcfHeader splits structured header fields on '=' without respecting double-quoted values, silently truncating Description strings that contain '=' (e.g. VRS version=2.0.1). Add .parseVcfHeaderBody() and .parseRawVcfHeader() to re-parse raw header text and patch each DataFrame back to the correct values. Fixes Bioconductor#80, fixes Bioconductor#89
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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