Port Parser.t (v2 paradigm, Tier 3)#171
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Per-test placement (per `porting-tests/detailed_plans/Parser.md`): - `src/allele.rs::tests::port_parser_*` (4 tests): subtests #17 (GA/GT minimise via `vcf_to_vep_allele`), #18/#19 (MNV-preserves-suffix — documented divergence from Perl's broader trim per Ensembl-Variation `trim_sequences()` rule at allele.rs:300-302), Axis B B1 (degenerate same-allele input collapses to "-/-" under MNV rule). - `src/transcript_consequence.rs::tests::port_parser_*` (3 tests): subtests #31 (bare chrom in valid set), #32 (`chr` prefix stripped by `normalize_chrom` then matches), #34 (unknown chrom rejected). - `tests/port_parser.rs` (4 tests): subtests #7 (nonexistent path — catches panic from `object_storage.rs:183` unwrap), #12 (gzipped VCF reads), #57 (CRLF line endings tolerated), Axis B B3 (`.vcf.bgz` extension routes through gzip reader). Axis B B2 (`buffer_variant_bounds` multi-chrom first-chrom-wins) is cross-referenced — already covered by `src/annotate_provider.rs::tests::port_input_buffer_axisB1_buffer_variant_bounds_multi_chrom_binds_to_first_chrom`. Coverage parity: 12 / 77 Perl-denominator unit-ports (incl. 3 Axis B); 47 architectural-no-analogue rows documented inline in `tests/port_parser.rs` (multi-format Parser base class, `validate_vf` warning emission, lowercase coercion, DB mode/LRG, 27 `detect_format` / STDIN / factory-dispatch rows); 21 blocked-future-work rows as commented-out stubs (all fold into existing future-work-vepyr.md entries — SO-term cluster engine blocker #2 × 6, chromosome-synonyms × 4, check_ref × 5, lookup_ref × 4, Uploaded_variation × 1, chr_filter × 1). **0 new future-work entries created**. v2 paradigm anchors: ~/.claude/skills/port-to-vepyr/references/v2-paradigm.md - sztywno 1:1: every Perl subtest gets a Rust analogue (test or documented stub). - standalone: no docker, no golden.vcf, no run_and_compare_csq. cargo test: 11 active passing tests across the 3 files; full lib suite 834 passed / 0 failed. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
v2-paradigm port of
ensembl-vep/t/Parser.t(Tier 3 PORT row 8 inporting-tests/port-status.md). Implements the 9 Axis A unit-ports + 3Axis B unit-ports identified in
porting-tests/detailed_plans/Parser.md(post-Phase-D audit 2026-05-27).
11 active tests across 3 files (B2 cross-references InputBuffer test):
src/allele.rs::tests::port_parser_*(4): subtest Add cluster, complement, and subtract UDTVFs #17GA/GTminimisevia
vcf_to_vep_allele; Replace std HashMap with AHashMap in interval_join.rs build map #18/Replace std HashMap with AHashMap in pileup events/coverage contig maps #19 MNV-preserves-suffix divergencedocumented (vepyr per Ensembl-Variation
trim_sequences()canonallele.rs:300-302); Axis B B1 degenerate same-allele.src/transcript_consequence.rs::tests::port_parser_*(3): subtestsFeature/optimize unnest groupby #31/vep: optimize VariantLookupExec exact parquet path to recover chr1 regression #32/ranges: restore safe join selection and residual interval filtering #34 —
_have_chrvianormalize_chrom+ valid-setmembership.
tests/port_parser.rs(4): Bump actions/checkout from 4 to 6 #7 nonexistent-path-errors (catches panicfrom
bio-format-core/object_storage.rs:183unwrap); Optimize coverage/count_overlaps execution and reduce allocations #12 gzipped VCFreads; Support individual annotation flag toggles (symbol, canonical, regulatory, etc.) #57 CRLF line endings tolerated; Axis B B3
.vcf.bgzextension.Coverage: 12/77 = 16% Perl-denominator (incl. 3 Axis B); 39%
addressable once engine blockers land. 47 architectural-no-analogue
rows + 21 blocked-future-work rows documented as comment blocks /
commented stubs in
tests/port_parser.rs. 0 new future-workentries created — all 21 blocked rows fold into 6 existing
porting-tests/future-work-vepyr.mdentries.Companion porting-tests update:
biodatageeks/vepyr-porting-testscommit
d4d8c51(joint with Cache_Variation flip) +518df9e(counter fix to 10/49 = 20%).
Test plan
cargo test -p datafusion-bio-function-vep --lib— 834 passedcargo test -p datafusion-bio-function-vep --test port_parser—4 passed
cargo test -p datafusion-bio-function-vep --tests(release) —full integration regression passed
port_input_buffer,port_annotation_source_adaptor— pass🤖 Generated with Claude Code