Yeliztli good first issues (Python)

cleanup: dead code — ImputePersistResult.quality in analysis/imputation_persist.py is a write-only dataclass field (populated once, never read; needed scalar already extracted to n_imputed) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — PRIORITY_GENES / CANCER_PANEL_GENES / CARDIO_PANEL_GENES in utils/uniprot.py are orphaned (sole consumer removed by #1001; only a self-validating test class remains) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — _compute_sha256 + LoadStats.sha256 in annotation/gnomad.py are orphaned (sole caller/writer removed by #553; no consumer left) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — _IN_BATCH_SIZE in api/routes/variant_detail.py is defined but never used (dead copy of vep_bundle.py's batching constant; the detail route does single-rsid lookups) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — _CPIC_CLASSIFICATION_STARS in backend/analysis/pharmacogenomics.py — superseded duplicate of evidence._CPIC_STARS, never read 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — parse_gnomad_vcf_line() is an orphaned single-record wrapper with no production caller (multiallelic ALT-drop hazard) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — carriage_map in analysis/hla_resolver.py:161 has no production caller (batch wrapper never adopted; consumers call carries_allele directly) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — RiskAssessment.readouts in analysis/risk_genotype.py is a write-only dataclass field (populated once at construction, never read; same class as #635/#647) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — RunResponse.compound_het_detected in api/routes/methylation.py is a dead response field (computed & serialized but never read; compound-het is surfaced via the live PathwaysResponse.compound_het) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — DEFAULT_REGIONS in scripts/lai_bundle_v2/06f_select_heldout.py is defined but never used (copy of 04c's argparse default; 06f derives regions from the sample map) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — EVIDENCE_LABELS in analysis/evidence.py has no consumer and has drifted from the shipped frontend labels (only a tautological test references it) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — _read_sample_file_format in services/lai_coverage_gate.py has no caller (sole call site inlined by #1145; live same-named copies take an Engine) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — DBNSFP_FIELDS in annotation/dbnsfp.py:89 has no production consumer (dead catalog; lookup_dbnsfp_by_rsids hardcodes the columns; #527 sibling) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — unused private constant _PANELS_DIR in analysis/risk_genotype.py:51 (referenced nowhere; load_risk_panel is path-parameterized; the test _PANELS_DIRs are unrelated locals) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — infer_panel_af_chrom (+ its private _AF_FILENAME_RE) in annotation/imputation_panel_af.py has no caller (dead inverse of the live chrom→path panel_af_path) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — engine_available in analysis/imputation_engine.py:41 has no caller (each engine runner reimplements its 'not missing_binaries(...)' predicate locally) 4 months ago

good first issue dead-code

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

cleanup: dead code — GNOMAD_BITMASK / DBNSFP_BITMASK duplicate engine.py's canonical GNOMAD_BIT / DBNSFP_BIT and have no production consumer 4 months 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) 4 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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 5 months 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) 5 months 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) 5 months 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) 5 months 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 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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) 5 months 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 5 months ago

bug good first issue

bioedca/Yeliztli

0

Personal genomics analysis platform for 23andMe raw data

Python

bioedca/Yeliztli

Open Issues Need Help