test(port-parser-vcf): v2 port (re-dispatch) — 15 active tests + 47 blocked-future-work stanzas#174
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test(port-parser-vcf): v2 port (re-dispatch) — 15 active tests + 47 blocked-future-work stanzas#174sitekwb wants to merge 2 commits into
sitekwb wants to merge 2 commits into
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…le.rs (sztywno 1:1)
Re-dispatch of Parser_VCF.t v2 port (original implementer aa08eb3a stalled).
Adds 9 #[test] functions in src/allele.rs::tests pinning the pure-fn allele
helpers against Perl Parser_VCF.t subtests:
pvcf_09_deletion_ac_to_a — vcf_to_vep_allele("AC","A")==("C","-")
pvcf_10_insertion_a_to_ac — vcf_to_vep_allele("A","AC")==("-","C")
pvcf_11_short_form_del_ignores_svtype — SVTYPE=DEL ignored on short-form
pvcf_12_short_form_ins_ignores_svlen — SVLEN=1 ignored on short-form
pvcf_13_multi_alt_snv_pass_through — SNV-only multi-ALT no-trim rule
pvcf_14_multi_alt_different_first_base — joint prefix=0
pvcf_15_multi_alt_same_first_base — joint prefix=1, REF→"-", pos shifts
pvcf_24_minimal_non_minimisable_multi_alt_pass_through — mixed-length pass-through
pvcf_23_a2_minimal_outcome_via_always_on_trimming — Q3 reclass: CAT→CCT
yields A/C via trim_sequences_ensembl (Perl minimal=1 equivalent); also
documents the API split between vcf_to_vep_allele (MNV-preserving) and
trim_sequences_ensembl (full minimizer).
Per-port plan: porting-tests/plans/2026-05-28-port-parser-vcf.md.
Detailed plan: porting-tests/detailed_plans/Parser_VCF.md (post-Phase-D).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
… blocked-future-work
New file tests/port_parser_vcf.rs covers the non-unit-port slice of
Parser_VCF.t v2 port:
6 active #[tokio::test] integration tests (use noodles VcfTableProvider):
pvcf_05_06_07_basic_parse_and_headers — header preservation + rows 0/1
pvcf_08_non_variant_rows_kept_in_batch_null_alt — vepyr keeps non-variant
rows at parser level (annotate-time skip downstream; documented deviation)
pvcf_16_stubby_row_parses — minimal-INFO row parses as SNV
pvcf_18_non_variant_row_default_kept_with_null_alt — default-mode keep
pvcf_69_non_numeric_pos_row_dropped_or_errored — noodles errors on bad POS
pvcf_a1_b1_star_allele_in_multi_alt_parsed_to_both_alts — A1/B1 Phase D row
6 architectural-no-analogue rows documented at top:
#3 (Parser::VCF Rust class), #4 (parser accessor),
#19/#21/#22 (* allele_string preservation), #23 (minimal=1 flag).
47 blocked-future-work stanzas at bottom, organized in 13 clusters per
the detailed_plan (SV/max_sv_size/CPX/ME/CNV/BND/TR/GP/individual/
individual_zyg/allow_non_variant/dont_skip/<DEL:*>). Each stanza names
the Perl row, the vepyr gap, the engine blocker # or sub-blocker, the
future-work-vepyr.md entry title, and a commented-out test body.
Per-port plan: porting-tests/plans/2026-05-28-port-parser-vcf.md.
Detailed plan: porting-tests/detailed_plans/Parser_VCF.md (post-Phase-D).
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_VCF.t(Parser_VCF). This is a re-dispatch — the original implementer (commit aa08eb3a) stalled mid-cargo-compile without committing any work; the dead branchport-parser-vcf-2026-05-28has only dev-test merges. This PR is on a fresh branch.Scope (per
porting-tests/detailed_plans/Parser_VCF.mdpost-Phase-D):#[test]functions insrc/allele.rs::testscovering 8 pure-fn unit-port rows (Bump futures from 0.3.31 to 0.3.32 #9-Add optional distance column to nearest UDTF #15, Bump Datafusion to 52 #24) + 1 reclassified row (feat: Ensembl VEP port #23 + Axis A2 combined per user Q3 decision 2026-05-28).#[tokio::test]functions intests/port_parser_vcf.rscovering noodles-reader integration rows (Bump softprops/action-gh-release from 1 to 2 #5/Bump actions/cache from 4 to 5 #6/Bump actions/checkout from 4 to 6 #7 consolidated, build(deps): bump datafusion from 50.3.0 to 51.0.0 in the datafusion group across 1 directory #8, Add overlap and merge UDTVFs #16, Replace std HashMap with AHashMap in interval_join.rs build map #18, CacheBuilder: no actual parallelism — sequential loops + execute_stream() merges partitions #69, Axis A1/B1 consolidated).tests/port_parser_vcf.rs) for blocked-future-work rows, organized into 13 clusters per the detailed_plan and naming engine blocker Add max_batch_rows option to PileupConfig for chunked streaming output #2 sub-entries by title.tests/port_parser_vcf.rs(Add Claude Code GitHub Workflow #3, Add new crate: datafusion-bio-function-ranges (coverage & count_overlaps) #4, Replace std HashMap with AHashMap in pileup events/coverage contig maps #19, feat: Preserve extra columns in cluster and subtract UDTFs #21, Add bio-function-vep crate with lookup_variants table function #22, feat: Ensembl VEP port #23).use_ok) — cargo handles.Total Perl coverage: 71 sztywno-1:1 rows (68 substantive + 2 Axis A + 1 Axis B) mapped → 15 active Rust tests + 47 commented future-work + 6 doc-only = 100% sztywno-1:1.
Test plan
env -u CONDA_PREFIX cargo test -p datafusion-bio-function-vep --lib pvcf→ 9 passingenv -u CONDA_PREFIX cargo test -p datafusion-bio-function-vep --test port_parser_vcf→ 6 passing#[cfg(test)] mod testsblock or new test filegolden.vcf, noport_common::run_and_compare_csq, nogen_golden.sh, nomod port_common(v2 standalone rule)dev-test(per user hard rule: no master/main targets in vepyr repos)Notes on Q3 reclassification (row #23)
Per user decision 2026-05-28 the Perl
minimal=1flag testCAT/CCT → A/Cis reclassified architectural-no-analogue → unit-port. vepyr exposes two trim helpers:vcf_to_vep_allele(allele.rs:283): MNV-preserving — same-length REF/ALT prefix-trim only, no suffix-trim. CAT/CCT → AT/CT.trim_sequences_ensembl(allele.rs:118): full minimizer used by Perlminimal=1. CAT/CCT → A/C with pos+1 / end+1.The test
pvcf_23_a2_minimal_outcome_via_always_on_trimmingasserts BOTH outcomes — documenting the API split and pinning the semantic equivalence with Perlminimal=1.Related
port-parser-vcf-redispatch-plan-2026-05-28)/" + 12 misc cluster entries (all already in place; no future-work-vepyr.md modification required by this port)🤖 Generated with Claude Code