Issues

• Public annotated mitochondrial ORFs lose the genetic-code declaration

  openvax/orfdata#203 · Filter by author iskandr opened on Nov 8, 2026

• The bundled uorf-evidence catalogue duplicates the uORF records already in orf-evidence

  openvax/orfdata#201 · Filter by author iskandr opened on Nov 7, 2026

• Tab completion (argcomplete) and the shared subtle help colors for the orfdata command line

  openvax/orfdata#195 · Filter by author iskandr opened on Nov 3, 2026

• Align orfdata with the openvax stack baseline (unused runtime biotite dependency, Biopython in tools, no develop.sh)

  openvax/orfdata#194 · Filter by author iskandr opened on Nov 3, 2026
  1

• Record-model and measurement helpers are private but imported across modules (_species, _contig, _Record)

  openvax/orfdata#193 · Filter by author iskandr opened on Nov 3, 2026

• Five hand-written GTF readers disagree on attribute parsing and malformed rows

  openvax/orfdata#192 · Filter by author iskandr opened on Nov 3, 2026

• CatalogRegistry and DatasetRegistry duplicate version resolution, species filtering and build-receipt checks

  openvax/orfdata#185 · Filter by author iskandr opened on Nov 2, 2026

• build.py downloads rebuild inputs without DataCache: no atomic write, truncated files fail checksum until deleted

  openvax/orfdata#184 · Filter by author iskandr opened on Nov 2, 2026

• Several per-source FASTA parsers duplicate fasta.read_fasta

  openvax/orfdata#182 · Filter by author iskandr opened on Nov 2, 2026

• Deferred review findings from the CLI and download PR series

  enhancement
  openvax/orfdata#173 · Filter by author iskandr opened on Oct 31, 2026

• CLI dispatch duplicates the command table and exposes a test hook

  enhancement
  openvax/orfdata#166 · Filter by author iskandr opened on Oct 30, 2026

• proteome --json and lift --json write JSON to stderr

  enhancement
  openvax/orfdata#165 · Filter by author iskandr opened on Oct 30, 2026

• Use one status vocabulary across data commands, catalogues, datasets and setup

  enhancement
  openvax/orfdata#164 · Filter by author iskandr opened on Oct 30, 2026

• Shared options differ between command groups

  bug
  openvax/orfdata#163 · Filter by author iskandr opened on Oct 30, 2026
  1

• Consolidate the acquisition commands onto data fetch

  enhancement
  openvax/orfdata#162 · Filter by author iskandr opened on Oct 30, 2026

• Acquire every resource kind through one interface instead of per-kind branches

  enhancement
  openvax/orfdata#161 · Filter by author iskandr opened on Oct 30, 2026

• Show species, sizes and default versions in data list and data info

  enhancement
  openvax/orfdata#160 · Filter by author iskandr opened on Oct 30, 2026

• Move viral collections onto DataCache's download/build split

  enhancement
  openvax/orfdata#159 · Filter by author iskandr opened on Oct 30, 2026

• Reuse pinned source files across builds and setup runs

  enhancement
  openvax/orfdata#157 · Filter by author iskandr opened on Oct 30, 2026

• Resume interrupted downloads of multi-gigabyte artifacts

  enhancement
  openvax/orfdata#156 · Filter by author iskandr opened on Oct 30, 2026
  1

• Nested Proteome layer metadata can leave a stale cached identity

  openvax/orfdata#145 · Filter by author iskandr opened on Oct 30, 2026

• Curate host associations and virus-type hierarchy across the viral reference panel

  openvax/orfdata#104 · Filter by author iskandr opened on Oct 16, 2026
  2

• Add Merkel cell polyomavirus and SV40 coding references with distinct cancer evidence

  openvax/orfdata#98 · Filter by author iskandr opened on Oct 15, 2026

• Add HTLV-1 and GDC HIV coding references with source-defined translation paths

  openvax/orfdata#97 · Filter by author iskandr opened on Oct 15, 2026

• Import CMV coding references with explicit strain and annotation coverage

  openvax/orfdata#95 · Filter by author iskandr opened on Oct 15, 2026