refactor(dada): dedup ASV serialization across dada handlers (#13)#31
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…pseudo (#13) Hoist the per-handler-local `AsvEntry` and `DadaStats` structs to module level and extract the duplicated cluster→ASV conversion and JSON serialization into shared helpers: - `birth_type_str()` — the 4-arm BirthType match (was duplicated 3x) - `asv_entry_from_cluster()` — decode + birth_type + field copy; takes `abundance` explicitly so the pooled path passes its recomputed per-sample read count (was duplicated 3x) - `to_json()` — compact-vs-pretty serialization (was duplicated 3x) No behavioral change: output JSON schema and values are byte-identical. Net -67 lines. The single-input `dada` handler keeps its own `DadaOutput` since it carries the aux-only fields. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
Addresses #13. During
dada-pooledcodegen, redundant code was flagged across thedadahandlers;dada-pseudohas since been added and is now folded into scope.This is a behavior-preserving dedup pass. Output JSON schema and values are byte-identical — verified by the existing
dada_from_fastq_matches_dada_from_derep_json,dada_multi_input_matches_per_file_runs, and pooled/pseudo determinism + downstream-feed tests.What changed
Hoisted the per-handler-local
AsvEntry/DadaStatsstructs to module level and extracted three duplicated blocks (each appeared 3×) into shared helpers:birth_type_str(&BirthType)— the 4-armBirthTypematchasv_entry_from_cluster(cluster, abundance)— decode + birth_type + field copy;abundanceis explicit so the pooled per-sample path passes its recomputed read countto_json(value, compact)— compact-vs-pretty serializationNet −67 lines (
62 insertions, 129 deletions).The single-input
dadahandler keeps its ownDadaOutputbecause it carries aux-only fields (ClusterStatJson/BirthSubJson/AuxJson); fully hoisting that would pull in the aux types for marginal gain.Deliberately out of scope
Lower-value / higher-churn items left for a possible follow-up: rayon pool-init boilerplate, the
[dada]/[dada-pooled]/[dada-pseudo]log tags, prior-FASTA loading, and sample-name resolution.Verification
cargo buildcleancargo clippyclean🤖 Generated with Claude Code