[geiresx]

GeiserX#313

Summary by CodeRabbit

• New Features

  • Archaic calls outside a genome’s mask or in excluded regions are retained as masked calls, with their alternate-allele count recorded.
  • Per-genome masks are supplied to IBDmix, allowing segments to span masked bases while still ending at masked homozygous mismatches.

• Documentation

  • Updated guidance for masked-call codes, mask handling, and rebuilding data after pin or mask changes.

[coderabbitai]

Caution

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Walkthrough

The archaic workflow now retains masked calls in tables, exports their positions as per-genome BED masks, and supplies those masks to IBDmix.

Changes: Archaic masked-call workflow

Layer / File(s)	Summary
Retain masked calls in archaic tables bin/archaic_report.py, docs/43-archaic.md, tests/test_archaic_report.py, tests/e2e/archaic-ancestry-1.sh	Known calls outside a genome’s mask or in excluded regions use codes 10–12. Included rows remain in the table. Tests check the codes and retained rows.
Export calls and per-genome masks bin/archaic_report.py, modules/local/archaic/main.nf, tests/test_archaic_report.py	The genotype step writes masked calls as their underlying 0–2 values and records masked positions in per-genome BED files. Tests cover mask intervals, empty masks, and invalid codes.
Pass masks to IBDmix modules/local/archaic/main.nf, scripts/43-archaic.sh, docs/43-archaic.md, tests/test_archaic_report.py	IBDmix receives a chromosome- and genome-specific mask with -r. Integration tests compare segment coverage for masked calls and unknown calls.

Estimated code review effort: 3 (Moderate) | ~25 minutes

Change: Bug fix

Possibly related PRs

• geiresx/OwnGenome#25: Updates the public-evidence workflow that runs step 43 and reports HG002’s Neanderthal total against the published range.

• Autofix · Keep fixing CodeRabbit findings and required CI, and resolving merge conflicts