Fix REFAA/VARAA returning NULL instead of empty AAStringSet for empty ranges#106

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jmg421:jarvis/issue-86

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(predictCoding): split refAA/varAA init + fix grepl regex for nonsense detection
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