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Pull requests: Bioconductor/VariantAnnotation

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Pull requests list

docs: warn about tabix seek cost with large which= in ScanVcfParam (#70)
#119 opened Jul 19, 2026 by jmg421 • Draft
1
1
fix: warn when multiple variants share a codon in predictCoding() (#46)
#118 opened Jul 19, 2026 by jmg421 Loading…
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feat: add Hedgehog property tests for readVcf roundtrip and predictCoding invariants (#113)
#117 opened Jul 18, 2026 by jmg421 Loading…
1
Add covr-based test coverage CI with Codecov reporting
#116 opened Jul 7, 2026 by Copilot AI • Draft
1
@vjcitn
1
fix: handle non-BGZF gzip VCFs from bcftools -Oz in readVcf (#32)
#112 opened Jul 7, 2026 by jmg421 Loading…
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3
fix: allow readVcf() to accept a connection (textConnection, url, etc.) (#28)
#111 opened Jul 7, 2026 by jmg421 Loading…
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fix: writeVcf.VRanges forwards info/filter/meta args to asVCF (#61)
#110 opened Jul 7, 2026 by jmg421 Loading…
1
fix: honour .vcf.gz suffix in writeVcf(index=TRUE) (#35)
#109 opened Jul 6, 2026 by jmg421 Loading…
1
fix: clarify which-arg accepted types (#34) and ... argument docs (#31)
#108 opened Jul 6, 2026 by jmg421 Loading…
2
docs: clarify REFCODON/VARCODON use transcript-strand coordinates (#43)
#105 opened Jul 6, 2026 by jmg421 Loading…
1
fix: preserve '*' spanning deletion alleles at read time (#65)
#104 opened Jul 1, 2026 by jmg421 Loading…
1
fix: strand-aware PRECEDEID/FOLLOWID for intergenic variants (#55)
#102 opened Jul 1, 2026 by jmg421 Loading…
1
fix: writeVcf preserves fileDate and suppresses bare contig lines (#78)
#101 opened Jul 1, 2026 by jmg421 Loading…
1
fix: expand() handles NULL geno data in sites-only VCFs (#72)
#100 opened Jul 1, 2026 by jmg421 Loading…
1
fix: expand() converts Number=A to Number=1 in headers (#79)
#99 opened Jul 1, 2026 by jmg421 Loading…
1
fix: locateVariants no longer silently drops intronic variants (#87)
#98 opened Jul 1, 2026 by jmg421 Loading…
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2
fix: predictCoding uses CDS-mapped width for exon/intron boundary deletions (#83)
#97 opened Jun 30, 2026 by jmg421 Loading…
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fix: DBS across codon boundary correctly classified as nonsense (#84)
#96 opened Jun 30, 2026 by jmg421 Loading…
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fix: expand() preserves non-standard rowRanges columns (#85)
#95 opened Jun 30, 2026 by jmg421 Loading…
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fix: locateVariants/predictCoding no longer silently drop large INDELs (#81)
#94 opened Jun 30, 2026 by jmg421 Loading…
1
fix: quote-aware VCF header parser preserves '=' in Description values (#80, #89)
#93 opened Jun 15, 2026 by jmg421 • Draft
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1
fix: predictCoding on empty ranges returns AAStringSet for REFAA/VARAA (#86)
#92 opened Jun 12, 2026 by jmg421 Loading…
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@lwaldron @vjcitn
6
Allow 'ANY' txdb, eg. EnsDb objects
#74 opened Nov 6, 2023 by mschubert Loading…
3
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