bioedca/Yeliztli

cleanup: dead code — GNOMAD_BITMASK / DBNSFP_BITMASK duplicate engine.py's canonical GNOMAD_BIT / DBNSFP_BIT and have no production consumer 34 minutes ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — CANCER_PRS_TRAITS in analysis/cancer_prs.py:54 has no production consumer (test-only oracle; runtime trait set is JSON-driven) about 2 hours ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — _HISTAMINE_RSIDS frozenset in analysis/allergy.py is never referenced (live histamine assessment uses inline per-rsID literals; flat membership set never fit; dead since the initial commit) 25 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — _HAPLOTYPE_TO_ALLELE dict in analysis/apoe.py is never referenced (orphaned per-haplotype map superseded by the unphased _DIPLOTYPE_TABLE; dead since the initial commit) 25 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — _NUMERIC_COLUMNS frozenset in query/translator.py is never referenced (precomputed 'for input validation' but no consumer; live sibling _TEXT_COLUMNS is wired, this isn't; dead since the initial commit) 25 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — record_gnomad_version in annotation/gnomad.py has no production caller (orphaned by the #553 cleanup; prod records via _record_db_version directly) 25 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — HIGH_IMPACT_CONSEQUENCES frozenset in analysis/rare_variant_finder.py is never read in production (consequence filter uses caller-supplied terms; only a tautological test consumes it) 25 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — parse_clinvar_vcf + load_clinvar_into_db in annotation/clinvar.py have no production caller (in-memory ingest pair superseded by the streaming iter_clinvar_vcf + load_clinvar_from_iter) 25 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — parse_gwas_tsv + load_gwas_into_db in annotation/gwas.py have no production caller (in-memory ingest pair superseded by streaming iter_gwas_tsv + load_gwas_from_iter; GWAS sibling of #891) 25 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — load_gnomad_from_csv / load_dbnsfp_from_csv / load_alphamissense_from_csv are reachable only from tests (production/build load native VCF/TSV; CSV is not an input; not in vulture baseline) 26 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — export_vcf_from_engine in ingestion/vcf_export.py has no production caller (test-only raw-variants VCF exporter; no route exposes it; not in vulture baseline) 26 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — lookup_gene_validity (singular) in annotation/clingen.py has no production caller (test-only wrapper; production batches via lookup_gene_validities; cf. #658/#667/#685) 26 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — classify_variant_rarity in annotation/gnomad.py has no production caller (pre-F15 global-AF classifier superseded by the popmax compute_rare_flags model; drags dead LOW_FREQUENCY_AF_THRESHOLD) 26 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — gwas.py public lookup API (lookup_gwas_by_rsids / lookup_gwas_traits_for_rsids / GWASAnnotationSet) is unused in production (consumers query gwas_associations directly; cf. cpic #667) 26 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — APOE position constants (APOE_RS429358_POS / APOE_RS7412_POS / APOE_CHROM) in analysis/apoe.py have no production reader; the #476 guard test is tautological 26 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — lookup_gene_constraint (singular) in analysis/gene_constraint.py has no production caller (test-only wrapper; production uses the batch lookup_gene_constraints + inline .get) 26 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — download_constraint / load_constraint_from_tsv (+ _load_rows/_row_to_record/GNOMAD_CONSTRAINT_URL) in annotation/gnomad_constraint.py are never called (pre-bundle path; superseded by load_constraint_from_csv) 26 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — create_dbnsfp_tables / create_gnomad_tables wrappers are test-only (loaders create table-then-index via private helpers for bulk-load perf; not in vulture baseline) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — is_lai_available() in analysis/lai.py has no production caller (test-only wrapper; gates use inline validate_lai_bundle+detect_java; resolves #647 open question) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — the entire cpic.py lookup_* helper family (6 functions) is uncalled in production (test-only; star-allele caller queries cpic tables directly via inline sa.select) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — LAIResult.is_available in analysis/lai.py is a constant-True field, never assigned or read (availability gated by is_lai_available()/runner instead) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — TraitsPanel.all_prs_rsids in analysis/traits.py is never called (sibling all_rsids is used; PRS rsids gathered via _load_prs_weight_sets instead) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — PreCheckResult.sample_name & UpdateResult.pre_check_results in db/update_manager.py are assigned but never read (semantic dead fields; ruff/vulture can't catch them) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — PathwayResult.pathway_description is assigned but never read across 8 analysis modules (semantic dead field; ruff/vulture can't catch it) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — download_and_load_gnomad / check_gnomad_update in annotation/gnomad.py are never called (pre-bundle ingest path; superseded by run_gnomad_bundle_update / check_gnomad_bundle_update) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — loe_rank + _LOE_RANK in analysis/pgx_guidelines.py are unused (transitively-dead; 'best-of aggregation downstream' never built; LoE attached as-is from CSV) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — count_deleterious in annotation/dbnsfp.py is a test-only wrapper over assess_ensemble (no production caller; engine uses deleterious_count field directly) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — _check_node_match in analysis/ancestry.py is a test-only back-compat shim over _classify_node_match (no production caller; superseded by the #165/#259 conflicting-SNP fix) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — most_severe_consequence / select_best_transcript in annotation/vep_bundle.py have no production caller (test-only; engine uses private _pick_best; vulture/#579 can't catch this) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — _POP_FIELDS INFO-field map in annotation/gnomad.py is never read (parse_gnomad_vcf_line hardcodes the fields; gnomAD twin of #527) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

Ancestry: "Population Ranking" shows bare, unlabeled centroid distances (lower = better) — misreads as bigger = better 28 days ago

bug good first issue

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — _TIER_ORDER tier-sort map in api/routes/variants.py is never used (consequence-summary sorts by count; nothing orders by impact tier) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — LoadingEmpty component in variant-table/EmptyStates.tsx is never rendered (VariantTable wires 4 of 5 states; loading is inline) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — ALL_CLINVAR_SIGNIFICANCE frozenset in rare_variant_finder.py is never read (filter uses the caller list directly; allowlist 'for filtering' unwired) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — unused dbNSFP column-mapping constants (_TSV_COLUMN_MAP/_SCORE_COLUMNS/_PRED_COLUMNS) in annotation/dbnsfp.py; the hand-written parser hardcodes them 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — 3 unused FHIR terminology constants in reports/fhir_export.py (SNOMED_SYSTEM, FHIR_GENOMICS_SYSTEM, LOINC_GENOMIC_REF_SEQ never referenced) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — unused list-based streaming generators _stream_csv/_stream_json in export.py (never called; superseded by _iter variants) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — useExecuteQuery hook in frontend query-builder.ts has no consumers (superseded by useRunQuery; remove its useInfiniteQuery import too) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — duplicated GTEX_PMID constant in annotation/gtex_eqtl.py is never read (live copy lives in analysis/gtex.py) 28 days ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — _delete_all_annotations in annotation/engine.py is never called (vestige of pre-F28 in-place crash recovery; superseded by the staging swap) 28 days ago

documentation good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

test: query-builder filter tests assert total_matching but not len(items) — empty/short items page passes vacuously 28 days ago

bug good first issue

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

Open Issues Need Help