v0.2.0

What's Changed

• perf(derep): deferred-division quals — store integer Phred sums, divide on demand (#23) by @cjfields in #24
• bench: add R derep-input mode (filenames vs preloaded objects) by @cjfields in #25
• feat(merge-pairs): --rescue-unmerged for non-overlapping pairs by @cjfields in #26
• fix(derep): fail loudly on u32 Phred-sum overflow instead of saturating (#23) by @cjfields in #27
• feat(io): default derep/sample JSON to compact + extension-driven gzip (#1) by @cjfields in #29
• bench: add reps (median ± spread) to compare_bench.py by @cjfields in #30
• refactor(dada): dedup ASV serialization across dada handlers (#13) by @cjfields in #31
• perf(mem): drop resident 16-bit k-mer vector from Raw, recompute on overflow (#32) by @cjfields in #34
• ci: R DADA2 concordance guardrail (warn-only) for Illumina + PacBio by @cjfields in #38
• perf(mem): shrink dada-pooled peak — free dead intermediates + integer merge accumulator (#39 steps 1-2) by @cjfields in #40
• perf(mem): stream derep→merge in dada-pooled, never hold all dereps (#41) by @cjfields in #42
• perf/mem: sparse kmer8 screen, gated to k≥8 (#43) by @cjfields in #45
• build: justfile/Makefile task runners with install + script reorg by @cjfields in #46
• docs: rename nav entry to "Building & installing" by @cjfields in #47
• feat(merge-pairs): input-file provenance + mismatch warning (#10) by @cjfields in #48
• Experimental WFA alignment backend (wfa2lib-rs), opt-in via --align-backend (#49) by @cjfields in #50
• Band the WFA aligner to match NW (fixes long-read O(n·s) blowup) (#51) by @cjfields in #52
• perf(wfa): edit-budget cap (--wfa-max-edits) to bound WFA on divergent pairs (#51) by @cjfields in #53
• feat: chimera-diagnostics — higher-order (trimera) screening by @cjfields in #54
• test(wfa): pin ends-free divergence (#102) + warn WFA concordance gates are fixture-scale by @cjfields in #56
• dev: isolated C++ WFA2-lib FFI oracle for #102 (no-ship) by @cjfields in #57
• dev: standalone compare_tables.py (ASV-table jaccard/count equivalence) by @cjfields in #58
• dev: kdist<->divergence calibration harness (KDIST_CUTOFF study) by @cjfields in #59
• feat(kdist-calibrate): --from-dada post-inference mode by @cjfields in #61
• feat(dada): add --failed-uniques diagnostic (issue #60) by @cjfields in #62
• crates.io publishing mechanics for v0.2.0 (issue #63) by @cjfields in #64

New Contributors

• @cjfields made their first contribution in #24

Full Changelog: v0.1.0...v0.2.0

v0.1.0

Initial crate release for Rust implementation of DADA2