All pull requests

Pull requests

• Fix ensemblVEP.Rmd: guard API-dependent chunks against Ensembl REST failures

  #121·lwaldron with CopilotAI opened Jul 28, 2026·

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• docs: warn about tabix seek cost with large which= in ScanVcfParam (#70)

  #119·jmg421 opened Jul 19, 2026Contributor·

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• fix: warn when multiple variants share a codon in predictCoding() (#46)

  #118·jmg421 opened Jul 19, 2026Contributor·

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• feat: add Hedgehog property tests for readVcf roundtrip and predictCoding invariants (#113)

  #117·jmg421 opened Jul 18, 2026Contributor·

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• Add covr-based test coverage CI with Codecov reporting

  #116·vjcitn with CopilotAI opened Jul 7, 2026·

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• fix: handle non-BGZF gzip VCFs from bcftools -Oz in readVcf (#32)

  #112·jmg421 opened Jul 7, 2026Contributor·

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• fix: allow readVcf() to accept a connection (textConnection, url, etc.) (#28)

  #111·jmg421 opened Jul 7, 2026Contributor·

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• fix: writeVcf.VRanges forwards info/filter/meta args to asVCF (#61)

  #110·jmg421 opened Jul 7, 2026Contributor·

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• fix: honour .vcf.gz suffix in writeVcf(index=TRUE) (#35)

  #109·jmg421 opened Jul 6, 2026Contributor·

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

  #108·jmg421 opened Jul 6, 2026Contributor·

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• docs: clarify REFCODON/VARCODON use transcript-strand coordinates (#43)

  #105·jmg421 opened Jul 6, 2026Contributor·

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• fix: preserve '*' spanning deletion alleles at read time (#65)

  #104·jmg421 opened Jul 1, 2026Contributor·

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• fix: strand-aware PRECEDEID/FOLLOWID for intergenic variants (#55)

  #102·jmg421 opened Jul 1, 2026Contributor·

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• fix: writeVcf preserves fileDate and suppresses bare contig lines (#78)

  #101·jmg421 opened Jul 1, 2026Contributor·

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• fix: expand() handles NULL geno data in sites-only VCFs (#72)

  #100·jmg421 opened Jul 1, 2026Contributor·

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• fix: expand() converts Number=A to Number=1 in headers (#79)

  #99·jmg421 opened Jul 1, 2026Contributor·

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• fix: locateVariants no longer silently drops intronic variants (#87)

  #98·jmg421 opened Jul 1, 2026Contributor·

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• fix: predictCoding uses CDS-mapped width for exon/intron boundary deletions (#83)

  #97·jmg421 opened Jun 30, 2026Contributor·

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• fix: DBS across codon boundary correctly classified as nonsense (#84)

  #96·jmg421 opened Jun 30, 2026Contributor·

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• fix: expand() preserves non-standard rowRanges columns (#85)

  #95·jmg421 opened Jun 30, 2026Contributor·

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• fix: locateVariants/predictCoding no longer silently drop large INDELs (#81)

  #94·jmg421 opened Jun 30, 2026Contributor·

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• fix: quote-aware VCF header parser preserves '=' in Description values (#80, #89)

  #93·jmg421 opened Jun 15, 2026Contributor·

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