Issues

• UCSC reference aliases name assemblies PyEnsembl doesn't have (galGal5, galGal6, canFam1, canFam2); ucsc_reference_names.py is empty

  openvax/varcode#737 · Filter by author iskandr opened on Nov 12, 2026

• Compatibility modules realized_effects.py and uorf.py have no users outside varcode and survived three major releases

  openvax/varcode#735 · Filter by author iskandr opened on Nov 12, 2026

• CI runs a starter-template flake8 step (one half can't fail) beside lint.sh, and installs an unused coveralls package

  openvax/varcode#734 · Filter by author iskandr opened on Nov 12, 2026

• Six human mitochondrial genes are always IncompleteTranscript: polyadenylation completes their stop codons

  openvax/varcode#731 · Filter by author iskandr opened on Nov 11, 2026
  1

• Test frameshift, stop-loss, partial and SV effects under non-standard genetic codes

  openvax/varcode#701 · Filter by author iskandr opened on Nov 4, 2026

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

  openvax/varcode#697 · Filter by author iskandr opened on Nov 3, 2026

• Deprecated aliases (load_vcf_fast, detect_loh, ensembl=, extended_protein_sequence) survive 11.0 and varcode still calls some of them

  openvax/varcode#693 · Filter by author iskandr opened on Nov 3, 2026
  3

• 29 underscore helpers are imported across module boundaries; effects/structural.py is 43 private functions around one public one

  openvax/varcode#692 · Filter by author iskandr opened on Nov 3, 2026

• DNA splice hypotheses miss the experimentally observed Ap2s1 del17 cryptic donor

  openvax/varcode#675 · Filter by author iskandr opened on Oct 30, 2026

• Expose a public finite registry or safe codec for native effect graphs

  openvax/varcode#674 · Filter by author iskandr opened on Oct 30, 2026

• Complete typed collection traversal and effect-model contracts

  openvax/varcode#653 · Filter by author iskandr opened on Oct 28, 2026
  3

• Discover variant-created ORF starts and extend partial-product annotation

  openvax/varcode#583 · Filter by author iskandr opened on Oct 8, 2026
  2

• Recover upstream acquisition provenance for legacy test fixtures

  openvax/varcode#571 · Filter by author iskandr opened on Oct 2, 2026

• Adopt the mhctools documentation style

  openvax/varcode#570 · Filter by author iskandr opened on Oct 2, 2026

• Remove tests that can't fail: fast-path self-comparison, Protocol isinstance checks, hasattr surveys

  openvax/varcode#479 · Filter by author iskandr opened on Sep 21, 2026
  2

• Interpret junctions, frameshifts, and extensions in mapped partial SV observations

  openvax/varcode#466 · Filter by author iskandr opened on Sep 18, 2026

• Adopt shared checksum-pinned osteosarc test assets for RNA-backed effect comparisons

  openvax/varcode#464 · Filter by author iskandr opened on Sep 18, 2026
  1

• CLI prints results as a logger repr on stdout; varcode and varcode-genes CSVs use different columns

  openvax/varcode#432 · Filter by author iskandr opened on Sep 15, 2026

• CHANGELOG: 2.3.1–5.0.6 have no sections; their notes are filed under 6.0.0

  openvax/varcode#411 · Filter by author iskandr opened on Sep 14, 2026

• Combine cis SNVs into MNVs without losing transcript or phase interpretations

  enhancement
  openvax/varcode#368 · Filter by author iskandr opened on May 11, 2026
  1

• [#271 stage 3 planning] SequenceDiffAnnotator design, naming, and reordered staging

  openvax/varcode#304 · Filter by author iskandr opened on Apr 15, 2026
  2

• Unified MultiOutcomeEffect / OutcomeSet generalization across splice, readthrough, germline, and RNA evidence

  openvax/varcode#299 · Filter by author iskandr opened on Apr 14, 2026

• ML-based splice prediction for variants outside canonical splice windows

  openvax/varcode#297 · Filter by author iskandr opened on Apr 14, 2026

• Foundational refactor: MutantTranscript abstraction

  openvax/varcode#271 · Filter by author iskandr opened on Apr 12, 2026

• Personal genome / haplotype-aware effect prediction (umbrella)

  openvax/varcode#270 · Filter by author iskandr opened on Apr 12, 2026