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refactor(pod5): remove dead run_info dedup code, unify reads-table builders - #434
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…ilders `utils/run_info.rs` reimplemented run_info dedup in a shape `merge`/`filter` no longer use (it was never wired into `utils/mod.rs`, zero call sites) — superseded by `pod5_assembler::deduplicate_run_infos` and never deleted. `build_reads_table`/`build_reads_table_remapped` had ~200 lines each of identical dictionary-collection/partition/concat/batch-write logic, differing only in input shape (owned pairs vs. borrowed `FlatReadRef`) — already abstracted at the per-row level by `PartitionRow`/`build_partition_inner`. Collapsed the surrounding skeleton into one generic `build_reads_table_generic` with both names as thin wrappers; no behavior or output change. Closes #433
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jayhesselberth
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Oct 6, 2026
Patch release. - Fixed: `merge` no longer produces non-portable output when inputs don't share one batch stride (#432) - Internal: dead run_info dedup removed, reads-table builders unified (#434) Version bump in root Cargo.toml (workspace + 5 path deps), CHANGELOG rolled, Cargo.lock regenerated; `cargo check --workspace` clean. Tag `v0.31.1` on the merge commit after merge (publishes to GitHub Releases and PyPI).
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Why
Follow-up to #432's merge batch-stride fix: an architecture review afterward
surveyed the rest of the workspace for the same cross-module layering smell
(a function stranded in one module that a sibling reaches into, or
near-duplicate logic copy-pasted across modules). Two findings, filed as
#433.
What
utils/run_info.rs—add_run_infos_deduplicated/map_run_info_indexwere never wired intoutils/mod.rsand have zerocall sites; superseded by
pod5_assembler::deduplicate_run_infos, whichmerge/filteralready share.build_reads_table(merge, owned(ReadData, Vec<u64>)pairs) andbuild_reads_table_remapped(filter, borrowedFlatReadRef) behind onegeneric
build_reads_table_generic<R: PartitionRow + Sync>. Both were~200-line copies of the same dictionary-collection/partition/concat/
batch-write skeleton, differing only in input shape — already abstracted
at the per-row level by the existing
PartitionRowtrait andbuild_partition_inner. Both public names stay as thin wrappers socallers in
merge.rs/operations/filter.rsare untouched.No behavior or output change — pure extraction, verified by the existing
test_merge_integration.rs/ filter / subset test suite (unchanged, allpassing) plus a full
cargo test -p escapepod-pod5run.Testing
cargo test -p escapepod-pod5: all green (incl. doctests)cargo fmt --all --check: cleanRUSTFLAGS=-Dwarnings cargo clippy --workspace --all-targets: cleanCloses #433