Issues

• Annotate alternative uORF frames and initiation-context mutations alongside canonical UTR effects

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

• Replace typechecks with isinstance checks and type annotations (and accept pathlib.Path)

  openvax/varcode#580 · Filter by author iskandr opened on Oct 7, 2026

• Transcript-model effect JSON loses realized candidates, hypotheses and products

  openvax/varcode#574 · Filter by author iskandr opened on Oct 5, 2026

• 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

• Effect strings in CSV: SpliceOutcomeSet hides alternatives, REF==ALT records become Silent p.335=, 1-bp deletions use a range

  openvax/varcode#436 · Filter by author iskandr opened on Sep 15, 2026

• UCSC unplaced contigs (chrUn_gl000216) aren't mapped, and one aborts annotation of the whole VCF

  openvax/varcode#435 · Filter by author iskandr opened on Sep 15, 2026
  1

• ReferenceMismatchError shows transcript-strand bases, so the mismatch reads backwards on minus-strand genes

  openvax/varcode#434 · Filter by author iskandr opened on Sep 15, 2026

• 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

• Design: one pipeline for splice, germline-phase, haplotype and SV effects (varcode 8)

  openvax/varcode#423 · Filter by author iskandr opened on Sep 15, 2026
  5

• Splice, germline-phase, haplotype and SV uncertainty don't compose

  openvax/varcode#421 · 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

• Structural variant effects() is very slow at some loci and for large typed SVs

  openvax/varcode#407 · Filter by author iskandr opened on Sep 11, 2026

• varcode.transforms.combine_cis_snvs — combine in-cis adjacent SNVs into MNVs

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

• Splice signal downgrade when germline already disrupts the signal

  enhancement
  openvax/varcode#363 · Filter by author iskandr opened on May 11, 2026

• [#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

• Boundary-codon reconstruction for exon skip protein math

  openvax/varcode#298 · 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

• Phasing: cis/trans-aware effect prediction for nearby variants

  openvax/varcode#269 · Filter by author iskandr opened on Apr 12, 2026