Issues

• Decide whether per-contig MAF chunks should be temp()

  performancequestion
  RILAB/argprep#44 · Filter by author rossibarra opened on Oct 7, 2026

• Test coverage gaps (backlog + 2026-10 review)

  tests
  RILAB/argprep#43 · Filter by author rossibarra opened on Oct 7, 2026

• Hardening: contig-collision override in split, strict MAF decoding

  bug
  RILAB/argprep#42 · Filter by author rossibarra opened on Oct 7, 2026

• Record summary_window_bp in report_stats.tsv and validate on read

  bug
  RILAB/argprep#41 · Filter by author rossibarra opened on Oct 7, 2026

• Docs drift: quality-BED parsing, v1.10 version refs, example options

  documentation
  RILAB/argprep#40 · Filter by author rossibarra opened on Oct 7, 2026

• maf_to_fasta.py: efficiency, nits, and test gaps

  performancetests
  RILAB/argprep#38 · Filter by author rossibarra opened on Oct 7, 2026

• Profile production runs and vectorize maf_to_sites hot loops

  performance
  RILAB/argprep#37 · Filter by author rossibarra opened on Oct 7, 2026

• Avoid rescanning every MAF at DAG-build time when contigs is unset

  bugperformance
  RILAB/argprep#36 · Filter by author rossibarra opened on Oct 7, 2026
  1

• Follow-ups for combined per-sample missing mask (#32)

  bugdocumentationtests
  RILAB/argprep#34 · Filter by author rossibarra opened on Oct 7, 2026
  1

• Up-front MAF quality metric evaluation

  RILAB/argprep#33 · Filter by author rossibarra opened on Oct 6, 2026
  2

• pg_gpu compatibility: haploid genotype encoding

  enhancement
  RILAB/argprep#31 · Filter by author rossibarra opened on Oct 5, 2026

• Emit per-contig accessible-regions BED (complement of mask)

  enhancement
  RILAB/argprep#30 · Filter by author rossibarra opened on Oct 5, 2026

• Native Relate haps/sample writer (if VCF conversion proves insufficient)

  enhancement
  RILAB/argprep#29 · Filter by author rossibarra opened on Oct 4, 2026

• Optional d4 format for quality-mask input and mask output

  enhancement
  RILAB/argprep#28 · Filter by author rossibarra opened on Oct 4, 2026

• Polarize variants with an ancestral FASTA

  enhancement
  RILAB/argprep#27 · Filter by author rossibarra opened on Oct 4, 2026

• Option to treat soft-masked MAF bases as missing

  enhancement
  RILAB/argprep#26 · Filter by author rossibarra opened on Oct 4, 2026
  1

• Separate indel gaps from other missing data in filters

  enhancement
  RILAB/argprep#25 · Filter by author rossibarra opened on Oct 4, 2026