All pull requests

Pull requests

• fix(nextflow): give the Nextflow report and couple screen the CYP21A2, dosage, gVCF and release data the bash path already uses

  #326·geiresx opened Nov 7, 2026Collaborator·

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  1

• fix(report): read every repeat, Y and phase result truthfully, and bring the docs and pins in line with 1.0.0

  #325·geiresx opened Nov 7, 2026Collaborator·

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  5

• fix(setup): size the Locityper k-mer table to the reference, repin TRExplorer, and test the steps that had no case

  #324·geiresx opened Nov 7, 2026Collaborator·

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  4

• fix(archaic): keep strict-mask sites marked and guard the chr22 Neanderthal share

  #323·geiresx opened Nov 7, 2026Collaborator·

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  1

• ci(e2e): cache GENCODE, test Locityper, and fail a case that checks nothing

  #322·geiresx opened Nov 6, 2026Collaborator·

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  16

• fix(contract): make the 1.0 output contract match where each file is written, and declare --pedigree

  #319·geiresx opened Nov 6, 2026Collaborator·

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  19

• fix(family): stop calling inherited chrX sites de novo, and lift chip mitochondrial sites correctly

  #316·geiresx opened Nov 6, 2026Collaborator·

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  3

• feat(rules): read the risk-allele and marker rows the catalog was missing

  #315·geiresx opened Nov 6, 2026Collaborator·

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  6

• fix(recheck): see image digest changes, never crash on a bad header, and lock the ClinVar refresh

  #314·geiresx opened Nov 6, 2026Collaborator·

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  1

• ci(release): refuse a tag that does not match the version, and ship curated 1.0.0 notes

  #312·geiresx opened Nov 6, 2026Collaborator·

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  1

• fix(sv): stop a filtered Manta record from hiding a real deletion, and read chrX depth by sex

  #311·geiresx opened Nov 6, 2026Collaborator·

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  11