nh13 · Oct 8, 2026
@@ -3,7 +3,7 @@ members = [".", "crates/fgumi-raw-bam", "crates/fgumi-dna", "crates/fgumi-bgzf",
 resolver = "2"
 
 [workspace.package]
-version = "0.7.0"
+version = "0.8.0"
 edition = "2024"
 rust-version = "1.93.0"
 repository = "https://github.com/fulcrumgenomics/fgumi"
@@ -20,22 +20,22 @@ license = "MIT"
 flate2 = { version = "1.1", features = ["zlib-rs"] }
 
 # Internal crates. Versions are bumped in lockstep by release-plz.
-fgumi-bam-io = { version = "0.7.0", path = "crates/fgumi-bam-io" }
-fgumi-bgzf = { version = "0.7.0", path = "crates/fgumi-bgzf" }
-fgumi-cli-common = { version = "0.7.0", path = "crates/fgumi-cli-common" }
-fgumi-cli-macros = { version = "0.7.0", path = "crates/fgumi-cli-macros" }
-fgumi-fmt = { version = "0.7.0", path = "crates/fgumi-fmt" }
-fgumi-consensus = { version = "0.7.0", path = "crates/fgumi-consensus", default-features = false }
-fgumi-dna = { version = "0.7.0", path = "crates/fgumi-dna" }
-fgumi-metrics = { version = "0.7.0", path = "crates/fgumi-metrics" }
-fgumi-pipeline-core = { version = "0.7.0", path = "crates/fgumi-pipeline-core" }
-fgumi-pipeline-io = { version = "0.7.0", path = "crates/fgumi-pipeline-io" }
-fgumi-raw-bam = { version = "0.7.0", path = "crates/fgumi-raw-bam" }
-fgumi-sam = { version = "0.7.0", path = "crates/fgumi-sam" }
-fgumi-simd-fastq = { version = "0.7.0", path = "crates/fgumi-simd-fastq" }
-fgumi-sort = { version = "0.7.0", path = "crates/fgumi-sort" }
-fgumi-tag = { version = "0.7.0", path = "crates/fgumi-tag" }
-fgumi-umi = { version = "0.7.0", path = "crates/fgumi-umi" }
+fgumi-bam-io = { version = "0.8.0", path = "crates/fgumi-bam-io" }
+fgumi-bgzf = { version = "0.8.0", path = "crates/fgumi-bgzf" }
+fgumi-cli-common = { version = "0.8.0", path = "crates/fgumi-cli-common" }
+fgumi-cli-macros = { version = "0.8.0", path = "crates/fgumi-cli-macros" }
+fgumi-fmt = { version = "0.8.0", path = "crates/fgumi-fmt" }
+fgumi-consensus = { version = "0.8.0", path = "crates/fgumi-consensus", default-features = false }
+fgumi-dna = { version = "0.8.0", path = "crates/fgumi-dna" }
+fgumi-metrics = { version = "0.8.0", path = "crates/fgumi-metrics" }
+fgumi-pipeline-core = { version = "0.8.0", path = "crates/fgumi-pipeline-core" }
+fgumi-pipeline-io = { version = "0.8.0", path = "crates/fgumi-pipeline-io" }
+fgumi-raw-bam = { version = "0.8.0", path = "crates/fgumi-raw-bam" }
+fgumi-sam = { version = "0.8.0", path = "crates/fgumi-sam" }
+fgumi-simd-fastq = { version = "0.8.0", path = "crates/fgumi-simd-fastq" }
+fgumi-sort = { version = "0.8.0", path = "crates/fgumi-sort" }
+fgumi-tag = { version = "0.8.0", path = "crates/fgumi-tag" }
+fgumi-umi = { version = "0.8.0", path = "crates/fgumi-umi" }
 
 # Third-party crates shared by two or more members. Declared once here so a member can
 # never drift onto a different version: two versions of a crate whose types cross crate

@@ -4,6 +4,33 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 
+## [0.8.0] - 2026-10-08
+
+### Bug Fixes
+
+- Point empty stdin/pipe input at the upstream stage ([#866](https://github.com/fulcrumgenomics/fgumi/pull/866))
+- Return an error instead of panicking on >65,535 libraries ([#956](https://github.com/fulcrumgenomics/fgumi/pull/956))
+- Add one @PG per command instead of one per chain leaf ([#1023](https://github.com/fulcrumgenomics/fgumi/pull/1023))
+- Propagate errors writing the final BGZF EOF block ([#1046](https://github.com/fulcrumgenomics/fgumi/pull/1046))
+
+### Features
+
+- Typed-step pipeline foundation ([#870](https://github.com/fulcrumgenomics/fgumi/pull/870))
+- Inline BAI indexer on the arena sink ([#883](https://github.com/fulcrumgenomics/fgumi/pull/883))
+- Restore --read-streams on the arena chain via a concurrent scatter reader ([#889](https://github.com/fulcrumgenomics/fgumi/pull/889))
+- Add the bam-roundtrip subcommand ([#936](https://github.com/fulcrumgenomics/fgumi/pull/936))
+
+### Performance
+
+- Drop the discarded decode key and add skippable input CRC ([#960](https://github.com/fulcrumgenomics/fgumi/pull/960))
+- Fold UMI-position cache into the group-key aux scan ([#976](https://github.com/fulcrumgenomics/fgumi/pull/976))
+
+### Refactor
+
+- [**breaking**] Remove the legacy unified_pipeline engine ([#947](https://github.com/fulcrumgenomics/fgumi/pull/947))
+
+<!-- generated by git-cliff -->
+
 ## [0.7.0] - 2026-08-24
 
 ### Bug Fixes

@@ -2,6 +2,19 @@
 
 All notable changes to this project will be documented in this file.
 
+## [0.8.0] - 2026-10-08
+
+### Features
+
+- Typed-step pipeline foundation ([#870](https://github.com/fulcrumgenomics/fgumi/pull/870))
+- Add --check-crc / --no-check-crc with the file-vs-stdin default ([#933](https://github.com/fulcrumgenomics/fgumi/pull/933))
+
+### Refactor
+
+- [**breaking**] Remove the legacy unified_pipeline engine ([#947](https://github.com/fulcrumgenomics/fgumi/pull/947))
+
+<!-- generated by git-cliff -->
+
 ## [0.7.0] - 2026-08-24
 
 ### Features

@@ -0,0 +1,7 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [0.8.0] - 2026-10-08
+
+<!-- generated by git-cliff -->
@@ -0,0 +1,7 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [0.8.0] - 2026-10-08
+
+<!-- generated by git-cliff -->
@@ -2,6 +2,37 @@
 
 All notable changes to this project will be documented in this file.
 
+## [0.8.0] - 2026-10-08
+
+### Bug Fixes
+
+- [**breaking**] Reject duplex/codec flags the callers never honor ([#997](https://github.com/fulcrumgenomics/fgumi/pull/997))
+  - `fgumi duplex --min-consensus-base-quality`, `fgumi codec --min-consensus-base-quality`, `fgumi codec --trim` and their `runall` forms are removed. `ConsensusCallingOptions` loses `trim` and `min_consensus_base_quality` (now in `QualityTrimOptions` / `MinConsensusBaseQualityOptions`); `DuplexOptions` loses `min_consensus_base_quality`; `CodecOptions` and
+- [**breaking**] Give each methylation consensus caller one SEQ convention and make filters, simulate and docs follow it ([#1010](https://github.com/fulcrumgenomics/fgumi/pull/1010))
+  - methylation::query_to_ref_positions takes the CIGAR as aligned (with its clips) and no longer takes the simplified CIGAR.  * fix(consensus)!: emit observed bases from simplex methylation consensus  Simplex EM-seq/TAPs consensus rewrote converted bases in the source reads (T->C / A->G at reference cytosines) before calling, so the emitted SEQ reported every site as unconverted. SEQ-based methylation callers and bisulfite-aware aligners read methylation from SEQ and saw every cytosine as methylated. The rewrite also hid real disagreements: all reads of a single-strand family copy one converted strand, so a C/T split is an error (or a UMI collision) and must lower quality like any other.  Consensus is now always called on the observed bases, and simplex emits them as they are, with the evidence in cu/ct. MM/ML are no longer emitted for simplex: MM can only describe bases present in SEQ, and a converted cytosine is not one. A simplex consensus also cannot tell a converted cytosine from a C>T mutation, so restoring it would assert a base the molecule may not have.  The shared MM builder now writes the SAM-spec '?' flag (unlisted bases are unknown), takes the conversion pattern from the read type (R1 C->T, R2 G->A) instead of the alignment strand, encodes each ML probability p as floor(256 p) capped at 255 (the SAM spec's [N/256, (N+1)/256) bins; it used floor(255 p), which put 1/2 and 3/4 in the bin below), and MN is available as a tag constant.
+- Keep MM/ML in step with hard-clipped and unmapped reads ([#1012](https://github.com/fulcrumgenomics/fgumi/pull/1012))
+- Classify dovetail FR pairs with coincident 5' ends as FR ([#1022](https://github.com/fulcrumgenomics/fgumi/pull/1022))
+- Decide read-level rejection before masking, and short-circuit templates like fgbio ([#1028](https://github.com/fulcrumgenomics/fgumi/pull/1028))
+- Handle NaN likelihoods like fgbio ([#1029](https://github.com/fulcrumgenomics/fgumi/pull/1029))
+- Truncate source-read cigars before converting hard clips, like fgbio ([#1042](https://github.com/fulcrumgenomics/fgumi/pull/1042))
+
+### Features
+
+- Typed-step pipeline foundation ([#870](https://github.com/fulcrumgenomics/fgumi/pull/870))
+
+### Performance
+
+- Use fixed-seed ahash on hot per-item maps to remove RandomState global-counter contention ([#865](https://github.com/fulcrumgenomics/fgumi/pull/865))
+- Single-pass scalar consensus-tag extraction ([#969](https://github.com/fulcrumgenomics/fgumi/pull/969))
+- Gated multi-base fast path for simplex consensus ([#973](https://github.com/fulcrumgenomics/fgumi/pull/973))
+
+### Testing
+
+- Speed up the slow-test tail without weakening invariants ([#881](https://github.com/fulcrumgenomics/fgumi/pull/881))
+- Pin read-order independence of alignment grouping ([#1037](https://github.com/fulcrumgenomics/fgumi/pull/1037))
+
+<!-- generated by git-cliff -->
+
 ## [0.7.0] - 2026-08-24
 
 ### Bug Fixes

@@ -2,6 +2,14 @@
 
 All notable changes to this project will be documented in this file.
 
+## [0.8.0] - 2026-10-08
+
+### Performance
+
+- Use fixed-seed ahash on hot per-item maps to remove RandomState global-counter contention ([#865](https://github.com/fulcrumgenomics/fgumi/pull/865))
+
+<!-- generated by git-cliff -->
+
 ## [0.7.0] - 2026-08-24
 
 <!-- generated by git-cliff -->

@@ -0,0 +1,7 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [0.8.0] - 2026-10-08
+
+<!-- generated by git-cliff -->
@@ -2,6 +2,25 @@
 
 All notable changes to this project will be documented in this file.
 
+## [0.8.0] - 2026-10-08
+
+### Documentation
+
+- Stop calling the duplication ladder a saturation curve ([#980](https://github.com/fulcrumgenomics/fgumi/pull/980))
+
+### Features
+
+- Produce --metrics on the multi-threaded chain path ([#915](https://github.com/fulcrumgenomics/fgumi/pull/915))
+- Compute consensus QC metrics inline in fused runall and standalone consensus ([#948](https://github.com/fulcrumgenomics/fgumi/pull/948))
+- [**breaking**] Publish metric column manifest; headered filter --stats ([#979](https://github.com/fulcrumgenomics/fgumi/pull/979))
+  - `fgumi filter --stats` now writes a headered fgbio-Metric TSV (a total_reads/passed_reads/failed_reads/pass_rate header row plus one data row) instead of the previous headerless two-column key/value layout. Column names and semantics are unchanged; downstream parsers of the old vertical format must be updated.  * test(metrics): round-trip conformance tests for all emitters  * feat(metrics): publish metric column manifest with contract tests  Adds crates/fgumi-metrics/metric_columns.json, the ordered column contract for every metric file fgumi emits, keyed <namespace>.<file> because group, simplex, duplex and dedup each write a differently shaped *.family_sizes.txt. tests/integration/test_metric_contract.rs parses the workspace with syn and fails in three cases: the manifest drifts from the live structs; a struct deriving serde's Serialize is neither listed nor explicitly allowlisted; or a serialized f64 field lacks the fgbio float encoding (Infinity/NaN rather than inf).  downsample's --histogram-kept/--histogram-rejected were hand-formatted with writeln!. They now serialize a DownsampleHistogramMetric through the shared writer, so they are covered by the contract. The output is byte-identical.  * fix(metrics): write headers for empty group and dedup histogram outputs  group (--family-size-histogram, and the --metrics family- and position-group-size histograms) and dedup (--metrics, --family-size-histogram, --duplication-ladder) wrote through a bare DelimFile, which emits the header lazily. An empty histogram or ladder was therefore a 0-byte file that fgbio's Metric.read rejects ("No header found"). Route them through the shared write_metrics, which always writes the header.  * docs(changelog): note filter --stats format break and metrics fixes  * fix(metrics): honor .gz, special-file and symlink destinations in write_metrics  write_metrics wrote rows to an extension-less temp file and renamed it into place. That had three problems. A .gz destination received plain text under a .gz name, which the metrics reader then failed to decompress. A non-regular destination such as /dev/stdout, a FIFO or a >(...) process substitution failed at rename time, after the whole run. A symlinked destination was replaced by a regular file.  The temp file now carries the destination's extension so compression follows it. Non-regular destinations are written in place. Symlinks are resolved before the atomic rename. Empty outputs derive their header from a plain scratch file, so the gzip path keeps its header too.
+
+### Testing
+
+- Fix inconsistent mate-strand flags in duplicate-group fixtures ([#908](https://github.com/fulcrumgenomics/fgumi/pull/908))
+
+<!-- generated by git-cliff -->
+
 ## [0.7.0] - 2026-08-24
 
 ### Bug Fixes

@@ -0,0 +1,26 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [0.8.0] - 2026-10-08
+
+### Features
+
+- Wire --pipeline-trace through the chain builder ([#937](https://github.com/fulcrumgenomics/fgumi/pull/937))
+- Thread-utilization and per-step bandwidth telemetry for the chain-builder engine ([#951](https://github.com/fulcrumgenomics/fgumi/pull/951))
+- Park idle pool workers to fix the thread-oversubscription cliff ([#955](https://github.com/fulcrumgenomics/fgumi/pull/955))
+- Add a refill-aware drain-first scheduler ([#986](https://github.com/fulcrumgenomics/fgumi/pull/986))
+
+### Performance
+
+- Don't fuse single-thread chains that declare Detached steps ([#884](https://github.com/fulcrumgenomics/fgumi/pull/884))
+
+### Refactor
+
+- [**breaking**] Remove the legacy unified_pipeline engine ([#947](https://github.com/fulcrumgenomics/fgumi/pull/947))
+
+### Testing
+
+- Read drained state once in pair-summer test steps ([#981](https://github.com/fulcrumgenomics/fgumi/pull/981))
+
+<!-- generated by git-cliff -->
@@ -0,0 +1,39 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [0.8.0] - 2026-10-08
+
+### Bug Fixes
+
+- [**breaking**] Enforce --max-temp-files on the arena spill path ([#993](https://github.com/fulcrumgenomics/fgumi/pull/993))
+  - fgumi-pipeline-io's SpillBlockEvent::Block gains a required key_kind field, and SpillWrite now emits SpillReady for its surviving runs at AllAnnounced (with slot_count set to their number) instead of as each run closes. RunMergerDyn::step takes a byte budget.
+- Leave no output files behind when a chain fails to build ([#1006](https://github.com/fulcrumgenomics/fgumi/pull/1006))
+
+### Features
+
+- Typed-step pipeline foundation ([#870](https://github.com/fulcrumgenomics/fgumi/pull/870))
+- Inline BAI indexer on the arena sink ([#883](https://github.com/fulcrumgenomics/fgumi/pull/883))
+- Route the sort command onto the declarative chain builder ([#885](https://github.com/fulcrumgenomics/fgumi/pull/885))
+- Restore --read-streams on the arena chain via a concurrent scatter reader ([#889](https://github.com/fulcrumgenomics/fgumi/pull/889))
+- Thread --sort-stats diagnostics through the chain ([#913](https://github.com/fulcrumgenomics/fgumi/pull/913))
+- Add --check-crc / --no-check-crc with the file-vs-stdin default ([#933](https://github.com/fulcrumgenomics/fgumi/pull/933))
+- Expose --block-batch and --file-granularity as hidden flags ([#943](https://github.com/fulcrumgenomics/fgumi/pull/943))
+- Thread-utilization and per-step bandwidth telemetry for the chain-builder engine ([#951](https://github.com/fulcrumgenomics/fgumi/pull/951))
+
+### Performance
+
+- Don't fuse single-thread chains that declare Detached steps ([#884](https://github.com/fulcrumgenomics/fgumi/pull/884))
+- Extend runs in the arena spill path (t16 parity) ([#886](https://github.com/fulcrumgenomics/fgumi/pull/886))
+- Parallel gather for the in-memory sort fast path ([#966](https://github.com/fulcrumgenomics/fgumi/pull/966))
+
+### Refactor
+
+- [**breaking**] Remove the legacy unified_pipeline engine ([#947](https://github.com/fulcrumgenomics/fgumi/pull/947))
+- Stop configuring the chain sort through RawExternalSorter ([#999](https://github.com/fulcrumgenomics/fgumi/pull/999))
+
+### Testing
+
+- Speed up the slow-test tail without weakening invariants ([#881](https://github.com/fulcrumgenomics/fgumi/pull/881))
+
+<!-- generated by git-cliff -->
@@ -2,6 +2,29 @@
 
 All notable changes to this project will be documented in this file.
 
+## [0.8.0] - 2026-10-08
+
+### Bug Fixes
+
+- Replace deprecated wide swizzle_relaxed with shuffle ([#992](https://github.com/fulcrumgenomics/fgumi/pull/992))
+- [**breaking**] Give each methylation consensus caller one SEQ convention and make filters, simulate and docs follow it ([#1010](https://github.com/fulcrumgenomics/fgumi/pull/1010))
+  - methylation::query_to_ref_positions takes the CIGAR as aligned (with its clips) and no longer takes the simplified CIGAR.  * fix(consensus)!: emit observed bases from simplex methylation consensus  Simplex EM-seq/TAPs consensus rewrote converted bases in the source reads (T->C / A->G at reference cytosines) before calling, so the emitted SEQ reported every site as unconverted. SEQ-based methylation callers and bisulfite-aware aligners read methylation from SEQ and saw every cytosine as methylated. The rewrite also hid real disagreements: all reads of a single-strand family copy one converted strand, so a C/T split is an error (or a UMI collision) and must lower quality like any other.  Consensus is now always called on the observed bases, and simplex emits them as they are, with the evidence in cu/ct. MM/ML are no longer emitted for simplex: MM can only describe bases present in SEQ, and a converted cytosine is not one. A simplex consensus also cannot tell a converted cytosine from a C>T mutation, so restoring it would assert a base the molecule may not have.  The shared MM builder now writes the SAM-spec '?' flag (unlisted bases are unknown), takes the conversion pattern from the read type (R1 C->T, R2 G->A) instead of the alignment strand, encodes each ML probability p as floor(256 p) capped at 255 (the SAM spec's [N/256, (N+1)/256) bins; it used floor(255 p), which put 1/2 and 3/4 in the bin below), and MN is available as a tag constant.
+- Classify dovetail FR pairs with coincident 5' ends as FR ([#1022](https://github.com/fulcrumgenomics/fgumi/pull/1022))
+- Truncate source-read cigars before converting hard clips, like fgbio ([#1042](https://github.com/fulcrumgenomics/fgumi/pull/1042))
+
+### Features
+
+- Typed-step pipeline foundation ([#870](https://github.com/fulcrumgenomics/fgumi/pull/870))
+- Declarative chain-builder layer + group --threads pilot ([#872](https://github.com/fulcrumgenomics/fgumi/pull/872))
+
+### Performance
+
+- Single-pass aux-tag rebuild (RawTagsEditor::rebuild_with) for zipper merge and NM/UQ/MD strip ([#962](https://github.com/fulcrumgenomics/fgumi/pull/962))
+- Fold per-record PG/AS/XS aux scans into single-pass walks ([#964](https://github.com/fulcrumgenomics/fgumi/pull/964))
+- Reduce serial-merge CPU and allocations at 1-2 threads ([#971](https://github.com/fulcrumgenomics/fgumi/pull/971))
+
+<!-- generated by git-cliff -->
+
 ## [0.7.0] - 2026-08-24
 
 ### Bug Fixes