fix: clarify which-arg accepted types (#34) and ... argument docs (#31)#108

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jmg421:fix/31-34-doc-clarifications

Commits on Jun 12, 2026

fix: predictCoding on empty ranges returns AAStringSet for REFAA/VARAA (#86)
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fix: use grepl() for stop-codon detection in predictCoding nonsense classification
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fix: clip large variants to transcript bounds before mapToTranscripts (#
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fix: filter empty GRangesList elements in locateVariants cache (#87)
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feat: expand() preserves non-standard rowRanges mcols (#85)
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fix: writeVcf preserves fileDate and suppresses bare contig lines for all-NA seqinfo (#78)
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Commits on Jun 15, 2026

fix: quote-aware VCF header parser preserves '=' in Description values (#80, #89)
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Commits on Jul 6, 2026

fix: clarify which-arg types (#34) and ... docs (#31) (closes #31, closes #34)
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