Issues

• Tests: extend VCF export coverage (diploid, mixed ploidy, metadata)

  testing
  RILAB/argtest#16 · Filter by author rossibarra opened on Oct 5, 2026

• Tests: content assertions in real Snakemake integration test

  testing
  RILAB/argtest#15 · Filter by author rossibarra opened on Oct 5, 2026

• Validation/coalescence plots: stream ts reloads and cache metrics

  performance
  RILAB/argtest#14 · Filter by author rossibarra opened on Oct 5, 2026

• Step 3: share traversal between observed and expected mutational load

  performance
  RILAB/argtest#13 · Filter by author rossibarra opened on Oct 5, 2026

• mutational_load(): single-pass implementation

  performance
  RILAB/argtest#12 · Filter by author rossibarra opened on Oct 5, 2026

• trim_samples: trim per sample node, not per individual (diploid over-trim)

  enhancement
  RILAB/argtest#11 · Filter by author rossibarra opened on Oct 5, 2026

• export_vcf: optional all-callable-bp (invariant site) mode

  enhancement
  RILAB/argtest#10 · Filter by author rossibarra opened on Oct 5, 2026

• Optional inferred-ARG example scored against true trees

  discussionenhancement
  RILAB/argtest#9 · Filter by author rossibarra opened on Oct 5, 2026

• Run check_mu_paths.py on real data (Gate 1)

  verification
  RILAB/argtest#8 · Filter by author rossibarra opened on Oct 5, 2026

• Run audit_arg_contract.py on real ARGs (possible duplicate-name trimming bug)

  bugverification
  RILAB/argtest#7 · Filter by author rossibarra opened on Oct 5, 2026

• Benchmark merge peak RSS: batched vs incremental concatenate

  performanceverification
  RILAB/argtest#6 · Filter by author rossibarra opened on Oct 5, 2026