feat(sort): route the sort command onto the declarative chain builder by nh13 · Pull Request #885 · fulcrumgenomics/fgumi

nh13 · 2026-08-30T21:10:38Z

Routes Sort::execute_sort onto the declarative chain/arena engine unconditionally (hand-built ChainSpec; SinkSpec::Bam/BamWithIndex per --write-index), keeping the owned RawExternalSorter in-tree as a parity oracle (its deletion is a later PR). Closes parity gaps: threading default, memory budget sized by max(threads, sort_threads), FGUMI_TMP_DIRS env fallback, owned-style Spill runs: summary wording.

Proves byte-identical output vs a saved baseline binary AND samtools (header-normalized) across all four sort orders + --write-index, spill and in-memory. Multi-thread: t4 −21%, t8 −15% vs owned (t16 was +3.4% here — the regression the stacked run-extension PR fixes).

Behavior change beyond sort: the shared source opener now rejects a records-only SAM with no @ header (previously accepted with an empty header) across every chain command — fail-closed on malformed input, since records reference reference IDs an empty header can't resolve.

Stacked on the t1-fix PR. Reviewed with a multi-agent gauntlet + a CodeRabbit-style pass; fixes in the final commit.

Risk: sort output changes are pinned by byte-level parity tests against a saved baseline and samtools; unsafe changes are none and the CLAUDE.md allowlist is unchanged; memory, thread, and backpressure policies change through max(threads, sort_threads) and bounded decoded-record output.

Route Sort::execute_sort through the declarative chain/arena engine.
Preserve RawExternalSorter as a parity oracle.
Support BAM output to stdout and SinkSpec::BamWithIndex.
Classify SAM input by content and reject records-only SAM with InvalidData.
Preserve temporary-directory fallback, spill behavior, CRC checks, and parse error context.
Add DecodedRecordBatchToRecordBatch for bounded, ordered sort ingestion with backpressure.
Add parity tests for sort orders, indexing, spilling, memory modes, flags, and invalid inputs.
Report spill counts as Spill runs.

coderabbitai · 2026-08-30T21:10:45Z

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Walkthrough

The sort command now uses the pipeline chain. SAM inputs bridge decoded records into sort ingestion. BAM sinks support stdout streams. Shared thread sizing and integration tests cover sorting, indexing, spilling, errors, and parity.

Changes

Sort pipeline cutover

Layer / File(s)	Summary
Input classification and output streaming `crates/fgumi-pipeline-io/src/sink/write_bgzf.rs`, `src/lib/pipeline/steps/source/mod.rs`, `src/lib/pipeline/steps/parse/sam.rs`	Plain BAM output can stream to `-` and `/dev/stdout`. SAM and extensionless inputs use content classification. SAM parsing requires a header and adds record-level error context.
SAM sort bridge and memory sizing `src/lib/pipeline/chains/builder.rs`, `src/lib/pipeline/steps/decoded_to_records.rs`, `src/lib/pipeline/steps/mod.rs`, `src/lib/commands/common.rs`	SAM sort-first inputs use `DecodedRecordBatchToRecordBatch`. Sort memory sizing uses the larger configured thread count. The adapter preserves record bytes and ordered backpressure behavior.
Chain-based sort execution `src/lib/commands/sort.rs`, `src/lib/pipeline/chains/commands/sort.rs`, `src/lib/commands/common.rs`	`execute_sort` builds a `ChainSpec` with sorting, temporary-directory, compression, CRC, threading, and indexing options. Unsupported non-default flags are logged as ignored. Sort summaries use `Spill runs`.
Sort cutover validation `tests/integration/test_sort_cutover_parity.rs`, `tests/integration/main.rs`, `tests/integration/test_chain_bam_with_index.rs`, `Cargo.toml`	Integration tests cover sort orders, parity, indexes, spills, temporary-directory propagation, invalid threads, inert flags, and corrupted BGZF input. The test dependency enables `noodles` BGZF access.

Estimated code review effort: 4 (Complex) | ~45 minutes

Merge Risk: 🔵 Low · up to 75b1c

When comparison tools are unavailable, the fallback test can accept correctly ordered output even if records are missing or changed, weakening protection against data-integrity regressions. The risk is bounded and mergeable with explicit owner follow-up.

Sequence Diagram(s)

sequenceDiagram
  participant CLI as Sort command
  participant Chain as Pipeline chain
  participant Adapter as DecodedRecordBatchToRecordBatch
  participant Sink as WriteBgzfFile
  participant Tests as Integration tests
  CLI->>Chain: build ChainSpec and execute sort
  Chain->>Adapter: convert SAM decoded batches
  Adapter->>Chain: provide ordered RecordBatch values
  Chain->>Sink: write sorted BAM and optional BAI
  Tests->>CLI: run sort scenarios and validate outputs

Suggested labels: fgumi sort

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title uses the required Conventional Commit format, includes the valid `sort` scope, uses a lowercase imperative description, and accurately describes the main change.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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nh13 · 2026-08-30T21:13:51Z

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codecov · 2026-08-30T21:19:20Z

Codecov Report

❌ Patch coverage is 93.98148% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.98%. Comparing base (2b346a0) to head (7eaaa3a).

Files with missing lines	Patch %	Lines
src/lib/pipeline/steps/decoded_to_records.rs	90.24%	8 Missing ⚠️
src/lib/commands/common.rs	88.88%	4 Missing ⚠️
src/lib/commands/sort.rs	96.77%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #885      +/-   ##
==========================================
+ Coverage   92.90%   92.98%   +0.08%     
==========================================
  Files         296      297       +1     
  Lines      149483   149627     +144     
==========================================
+ Hits       138876   139131     +255     
+ Misses      10607    10496     -111

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nh13 · 2026-08-31T05:15:01Z

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Inline comments:
In `@src/lib/commands/common.rs`:
- Line 1965: Protect each log-capture session with a separate session-level
mutex: acquire it before the CAPTURED_LOGS clear and retain the guard through
the captured() snapshot/assertion path. Do not reuse CAPTURED_LOGS for session
serialization, since CaptureLogger::log locks that buffer.

In `@src/lib/commands/sort.rs`:
- Around line 859-868: In src/lib/commands/sort.rs lines 859-868, change both
ignored-option notices in the sort command flow from info-level to warn-level
logging. In tests/integration/test_sort_cutover_parity.rs lines 1018-1019,
update cutover_inert_flags_do_not_error to run as a subprocess with
RUST_LOG=info and assert the ignored-flag notice appears in stderr while
preserving the existing count and order assertions.

Apply the same fix in `@tests/integration/test_sort_cutover_parity.rs` around
lines 1018 - 1019: The regression test should verify that ignored-flag notices
remain visible.

In `@tests/integration/test_sort_cutover_parity.rs`:
- Around line 119-129: Update the skip messages and documentation in the sort
cutover parity tests to remove references to a default baseline path, since
baseline_bin only consults FGUMI_BASELINE_BIN. Revise the sites around the
listed skip messages and doc paragraph to state that the environment variable is
unset or its configured file is unavailable, while preserving the existing skip
behavior.
- Around line 822-833: Run the nonspill Sort case through the same
subprocess-based execution path as the spill case, with RUST_LOG=info, and
capture its stderr; assert that the output does not contain “Spill runs:” before
comparing results, so the nonspill case verifies the default in-memory behavior.

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Cargo.toml
crates/fgumi-pipeline-io/src/sink/write_bgzf.rs
src/lib/commands/common.rs
src/lib/commands/sort.rs
src/lib/pipeline/chains/builder.rs
src/lib/pipeline/chains/commands/sort.rs
src/lib/pipeline/steps/decoded_to_records.rs
src/lib/pipeline/steps/mod.rs
src/lib/pipeline/steps/parse/sam.rs
src/lib/pipeline/steps/source/mod.rs
tests/integration/main.rs
tests/integration/test_chain_bam_with_index.rs
tests/integration/test_sort_cutover_parity.rs

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Matches the owned engine's memory_budget_threads. Also affects runall's sort stage when --sort::sort-threads exceeds --threads (intended: same semantics).

Routes Sort::execute_sort's execution onto the declarative chain builder (build_for(spec)?.run()) instead of the owned RawExternalSorter engine. The owned sorter is still built (self.build_sorter) but only to source the config banner's thread/temp-file numbers; execution itself goes through the chain. All guards and the config-banner logging are kept verbatim. Two owned-engine parity gaps surfaced once sort's default (always-on) execution path started depending on shared chain infrastructure for the first time, and both are fixed here as prerequisites to the cutover: - Stdout sink: WriteBgzfFile::new/new_with_handle (fgumi-pipeline-io) always called File::create, so `sort -o -` wrote a regular file literally named `-` instead of streaming BGZF to stdout. Routed both through open_output_writer (mirroring WriteRawFile's existing `-` handling and the owned sort engine's PooledBamWriter), boxing WriterState's writer so a non-seekable stdout handle fits the same field. BamWithIndex's stdout rejection in add_sink is untouched, so this only affects the plain BAM sink. - SAM source: ChainBuilder::add_source unconditionally rejected SAM input when sort was the first stage, on the incorrect premise that "the legacy sorter read BAM only" -- untrue for the owned RawExternalSorter, and sort's own CONTRACTS table (test_input_source_matrix) declares SAM support as required. Removed the rejection so SAM routes through the existing ParseSamChunk preamble like every other SAM ingest. That preamble emits DecodedRecordBatch, but the sort ingest (SortBuffer) needs RecordBatch, so added a DecodedRecordBatchToRecordBatch adapter step (mirrors TemplatesToRecordBatch) to bridge it. Two smaller gaps surfaced once SAM input started actually reaching this path for sort: InputSource's `.sam` suffix branch trusted the extension outright instead of sniffing content (so a BGZF file misnamed `.sam` failed to parse), and ParseSamChunk's record-read error wasn't labelled, so a malformed record surfaced as a bare "unexpected EOL" instead of naming it as a SAM record fault (now labelled the same way fgumi_bam_io::sam_input already labels the identical fault). Adds a smoke test (test_sort_cutover_parity.rs) verifying the command produces correctly coordinate-sorted output via the chain. This is not a genuine RED/GREEN pair -- the pre-cutover owned-engine path already sorts correctly, so it passes both before and after; the real parity gate is a follow-up task's byte-identity comparison against the owned-engine baseline. Full cargo ci-test (9561 tests) passes, including the 20 tests (across test_sort_thread_logging, test_streaming_output, test_sam_input, and test_input_source_matrix) that regressed during development of this cutover and are fixed by the two parity fixes above.

nh13 · 2026-08-31T15:52:24Z

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Inline comments:
In `@tests/integration/test_sort_cutover_parity.rs`:
- Around line 460-463: Remove the early no-oracle return in
cutover_matches_baseline_and_samtools so the sort cases still execute when both
the baseline and samtools are unavailable. In the samtools-unavailable Some(_)
arm, assert fgumi_verify_sorted(current_bin, current_out, flag) before emitting
the skip message, while preserving the existing cross-check behavior when
samtools is available.
- Around line 735-737: Add cutover parity cases covering records with an empty
CIGAR, an empty sequence, and zero-length qualities alongside the existing cases
in the test matrix. If equivalent coverage already exists in another sort
integration test, reference that coverage instead of duplicating cases.

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nh13 · 2026-08-31T16:52:29Z

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Inline comments:
In `@tests/integration/test_sort_cutover_parity.rs`:
- Around line 115-116: Update the Rust documentation comment near the
fallback-oracle guidance to describe that callers run `fgumi sort --verify` when
external oracles are unavailable, rather than requiring `samtools` or skipping
the case. Enclose referenced identifiers such as `samtools` and `fgumi sort
--verify` in backticks.
- Line 815: Strengthen the degenerate-record round-trip assertions in the
relevant test by comparing decoded output records against the expected
coordinate-sorted input records regardless of whether FGUMI_BASELINE_BIN is set.
Retain the count and sort-order checks, and ensure record fields such as CIGAR,
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nh13 · 2026-08-31T17:52:34Z

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In `@tests/integration/test_sort_cutover_parity.rs`:
- Around line 515-518: Strengthen the fallback assertions in the test around
fgumi_verify_sorted so they also compare input_bam and current_out as an
order-independent full-record multiset, preserving every record and its identity
even when FGUMI_BASELINE_BIN and samtools are unavailable.

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Address a multi-agent review of PR A (the execute_sort chain cutover): - Remove a committed personal absolute path used as a baseline-binary fallback in the parity test; the baseline now comes solely from FGUMI_BASELINE_BIN (a host-specific path must never live in the repo). - Fix a process-global logger collision: the standalone-sort summary test installed its own capturing logger, which panics under plain `cargo t` (one process, one global logger) when a sibling capture test in commands::common has already installed one. Both now share a single crate-wide `commands::common::test_log_capture` installer. - Give a queryname-lex parity case a real order oracle. It has no samtools equivalent, so it previously skipped entirely without a baseline; it now self-verifies with `fgumi sort --verify` (an accepted order oracle), so it is checked even in plain CI. - Surface the underlying OS error on output-open failure: WriteBgzfFile wrapped an anyhow error with `{e}`, dropping the source chain; use `{e:#}` so permission-denied / ENOENT reasons survive. - Warn that `--read-streams` / `--sort-stats` are not yet threaded through the chain rather than silently ignoring a non-default value (full restore tracked as follow-up). - Skip the per-record GroupKey computation for a SAM-first sort (the CIGAR walk + aux-tag extraction), which sort discards — the same cheap config the correct-first path already uses. Output-neutral: only the discarded key changes. - Single source of truth for the sort memory-budget thread count (common::sort_memory_budget_threads), shared by the owned banner path and the chain builder so they cannot drift; rename the mis-named budget test to what it actually checks; drop a redundant `output` re-bind and the duplicate "Sorting BAM" timer start line; fix a strip_pg_lines trailing-newline edge and a stale line-number comment. The headerless-SAM rejection this cutover introduced (records-only SAM, previously accepted with an empty header, now failing closed across all chain commands) is intentional and investigated; it is called out in the PR description as a cross-command behavior change.

The sort-command cutover (#885) hardcoded QueueMemoryOptions::default() (768 MiB/thread) when building the chain, so `fgumi sort --max-memory` bounded only the sorter's in-memory record buffer, not the bytes held in the inter-stage pipeline queues. A small --max-memory (e.g. -m 64K -@ 8) shrank the sort buffer while the queues could still use gigabytes, so peak RSS barely moved. Project the command's single memory knob (--max-memory / --memory-reserve / --memory-per-thread) onto the queue budget via a new queue_memory_options helper, so one flag bounds both budgets. The two totals scale by different thread counts (the sorter by max(threads, sort_threads), the queues by threads); that asymmetry is intentional and documented on the flag. Two deliberate, benign consequences of sharing the flag, documented in code and called out here: - The default queue budget now follows --max-memory's default ("768M" = 768 MB decimal via the size parser), marginally below the former hardcoded 768 MiB, aligning it with the sorter's own default. - A large or `auto` --max-memory does not balloon queue memory: the queue total does not raise the per-stage backpressure marks (512/256 MiB, issue #765), which are what bound in-flight queue bytes. Verified empirically: peak RSS is flat (~380-410 MiB) across -m 768M/auto/4GiB/8GiB at -@ 8 on a 64 GiB host. Extract the ChainSpec construction into a unit-tested build_sort_chain_spec so the wiring (queue budget, stages, threading, write-index sink) is guarded against a silent revert, not only exercised through a full run where a dropped knob is invisible.

The sort-on-chain cutover (#885) dropped the per-phase wall-time breakdown that every `fgumi sort` run used to log. Pre-cutover the owned `RawExternalSorter` engine emitted `=== Sort Phase Timing ===` (the tool CLAUDE.md's Benchmarking Notes call the primary sort attribution tool); standalone `fgumi sort` now runs entirely through the declarative chain and never calls that engine, so the block was gone and `--sort-stats` was repurposed to gate the k-way-merge scheduling counters instead. The chain still models every phase as a discrete step, and the runtime already records each step's cumulative busy time, so re-derive the breakdown as a roll-up over the end-of-run pipeline stats snapshot rather than resurrecting the retired engine: - Add `SortPhaseTimingFinalizeHook`, which maps each sort step name to its phase (read+decompress / in-memory sort / spill write / consolidation / k-way merge / write output), sums the per-step `total_run_ns` into phase buckets, and logs the block with per-phase seconds and percentages plus a note that the percentages are shares of cumulative per-step busy time (the steps run concurrently). It reads `snapshot.steps` only, never the `detached` view, which would double-count the detached writer. - Register it in `ChainBuilder::build` for any chain containing a sort stage, gated on a stats collector already being attached (`--pipeline-stats` / `FGUMI_PIPELINE_STATS=1`). The default sort path attaches no collector, so it keeps its zero-overhead behavior. - Update CLAUDE.md Benchmarking Notes: it described the now-dead owned-engine timer as always-on; document the chain-derived roll-up and its invocation, and note the library `fgumi-sort` engine still carries its own `SortPhaseTimer` for direct `RawExternalSorter` callers.

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fix(chains): size sort buffer by max(threads, sort_threads) in add_sort

39b26db

Matches the owned engine's memory_budget_threads. Also affects runall's sort stage when --sort::sort-threads exceeds --threads (intended: same semantics).

fix(chains): match owned engine's 'Spill runs:' summary wording

44f4584

test(sort): four-order cutover parity vs baseline binary and samtools

de9e04b

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nh13 added this pull request to the merge queue Aug 31, 2026

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nh13 deleted the nh/sort-chain-cutover branch August 31, 2026 18:21

This was referenced Aug 31, 2026

chore: release v0.8.0 #868

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fix(sort): thread --max-memory into the pipeline queue budget #888

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This was referenced Sep 1, 2026

feat(sort): restore --read-streams on the arena chain via a concurrent scatter reader #889

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refactor(sort): delete the CLI's throwaway sorter construction #890

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nh13 mentioned this pull request Sep 9, 2026

fix(sort): restore the === Sort Phase Timing === per-phase diagnostic #945

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