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feat(sort): inline BAI indexer on the arena sink - #883
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Included review availability: 0 reviews are currently available. Your included PR review attempts over the past 7 days set your current allowance at 1 review per hour. WalkthroughThe pipeline now builds BAM index manifests during BGZF compression and writes BAI sidecars inline. ChangesInline BAM indexing
Estimated code review effort: 4 (Complex) | ~60 minutes Merge Risk: 🔵 Low · up to The change builds and writes the BAM index inline after the BAM is finalized, which removes the reread pass but can leave a complete BAM beside an incomplete index if index creation fails. The PR is otherwise mergeable with explicit owner awareness of this bounded failure-mode risk. Sequence Diagram(s)sequenceDiagram
participant ChainBuilder
participant BgzfCompress
participant WriteBgzfFile
participant BaiBuilder
participant BAIFile
ChainBuilder->>BgzfCompress: Enable index_bam for BamWithIndex
BgzfCompress->>BgzfCompress: Parse BAM records and build BamIndexManifest
BgzfCompress->>WriteBgzfFile: Emit BGZF block and manifest
WriteBgzfFile->>BaiBuilder: Add records with cumulative offsets
WriteBgzfFile->>BAIFile: Write BAI after BGZF EOF and flush
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #883 +/- ##
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+ Coverage 92.71% 92.88% +0.17%
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Files 294 296 +2
Lines 148589 149417 +828
==========================================
+ Hits 137760 138786 +1026
+ Misses 10829 10631 -198 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Actionable comments posted: 5
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Inline comments:
In `@crates/fgumi-pipeline-io/src/sink/write_bgzf.rs`:
- Around line 631-635: The straddling test currently verifies only that one
reference sequence exists, not the joined index contents. Strengthen the
assertions after parsing the index in the straddling test to validate both
records’ expected bins and chunk start/end virtual offsets, using the manifest’s
fixed header length, phys_comp_len prefix sums, BGZF_MAX_BLOCK_SIZE, and uoffset
values; retain the existing reference-count check.
In `@crates/fgumi-pipeline-io/src/types.rs`:
- Around line 318-321: Update the assertion for indexed.heap_size() to verify
the exact expected sum of bytes.capacity() and the manifest’s heap contribution,
matching the contract and the pattern used by
heap_size_counts_allocated_capacity_not_logical_len, rather than only checking
that heap_size() is greater than bytes.capacity().
In `@src/lib/pipeline/chains/builder.rs`:
- Line 1450: Add the path returned by bai_sidecar_path(output_path) to the
output-collision validation before constructing the WriteBgzfFile sinks,
ensuring it is checked against rejects_path and other outputs. Keep the existing
sink construction unchanged after collisions are rejected.
In `@src/lib/pipeline/steps/chain_tests.rs`:
- Line 575: Strengthen the assertion in the test loop around the emitted
alignment entries: inspect each entry’s context and assert ref_id, start, end,
and is_mapped against expected values derived from the loop index, rather than
only checking ctx.is_some().
In `@tests/integration/test_chain_bam_with_index.rs`:
- Around line 420-425: Update the affected integration tests to execute each
chain and validate its inline .bai before checking samtools_available(). Keep
the samtools availability gate only around the parity assertions against
samtools, so the chain, sidecar, and parser are exercised even when samtools is
unavailable.
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crates/fgumi-bam-io/src/lib.rscrates/fgumi-bam-io/src/writer.rscrates/fgumi-pipeline-io/src/sink/write_bgzf.rscrates/fgumi-pipeline-io/src/sink/write_raw.rscrates/fgumi-pipeline-io/src/sort/arena_ingest.rscrates/fgumi-pipeline-io/src/sort/tests.rscrates/fgumi-pipeline-io/src/source/read_bam.rscrates/fgumi-pipeline-io/src/types.rssrc/lib/pipeline/chains/builder.rssrc/lib/pipeline/chains/commands/sort.rssrc/lib/pipeline/chains/finalize.rssrc/lib/pipeline/chains/sink_spec.rssrc/lib/pipeline/steps/bgzf/compress.rssrc/lib/pipeline/steps/chain_tests.rssrc/lib/pipeline/steps/tests.rssrc/lib/pipeline/steps/types.rstests/integration/main.rstests/integration/test_chain_bam_with_index.rs
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Actionable comments posted: 2
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Inline comments:
In `@crates/fgumi-pipeline-io/src/sink/write_bgzf.rs`:
- Around line 333-337: Update the BAI finalization path around write_bai_index
to write the generated index to a temporary file in the same directory, then
atomically rename it to sink.sidecar_path only after the write succeeds. Ensure
failures clean up or do not expose the temporary file, while preserving the
existing error propagation and success log.
In `@src/lib/pipeline/chains/builder.rs`:
- Around line 1449-1455: Move the bai_sidecar_path derivation and
reject_index_sidecar_collisions call ahead of write_step construction and
WriteBgzfFile::new, so all collision validation completes before any sink can
truncate files. Keep the derived sidecar path available for index attachment and
remove the later duplicate check.
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crates/fgumi-pipeline-io/src/sink/write_bgzf.rscrates/fgumi-pipeline-io/src/types.rssrc/lib/pipeline/chains/builder.rssrc/lib/pipeline/steps/chain_tests.rstests/integration/test_chain_bam_with_index.rs
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Inline comments:
In `@src/lib/pipeline/chains/validate.rs`:
- Line 315: Update validate_cross_stage_constraints to reject queryname and
template-coordinate terminal Stage::Sort orders when the sink is
SinkSpec::BamWithIndex, before sink construction; retain coordinate sorting as
valid. Add release-mode tests covering both rejected orders.
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crates/fgumi-bam-io/Cargo.tomlcrates/fgumi-bam-io/src/writer.rssrc/lib/pipeline/chains/builder.rssrc/lib/pipeline/chains/validate.rs
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Inline comments:
In `@src/lib/pipeline/chains/validate.rs`:
- Around line 340-345: Update validate_cross_stage_constraints to reject
SinkSpec::BamWithIndex targets that use stdout or any chain containing
Stage::Align before stage construction, covering Correct → Sort and Correct →
Align → Sort flows. Reuse the existing add_sink validation conditions where
possible, retain those checks as defense in depth, and ensure validation occurs
before add_correct can create or truncate a rejects WriteBgzfFile.
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src/lib/pipeline/chains/builder.rssrc/lib/pipeline/chains/validate.rs
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…ine BAI arena sink Extends the Task 6 chain-direct BamWithIndex test with the Task 7 correctness gate: idxstats/region-query parity against samtools' own index over placed, placed-but-unmapped, and truly-unplaced reads across multiple references; the same parity check forced through many physical BGZF blocks plus a record that straddles a block by itself; and a determinism + correctness check for the Detached writer (the only writer configuration reachable from a chain-direct BamWithIndex spec). fgumi sort --write-index does not yet route through this chain builder, so these tests build the ChainSpec directly rather than through the CLI.
…ndexer WriteBgzfFile::with_bai_index position-bins records purely by arrival order and never verifies @hd SO, unlike the retired IndexBamFinalizeHook which read back a SO:coordinate BAM via noodles::bam::fs::index. Document the precondition on the method, and add a debug_assert at the chain-builder wiring site (add_sink) as a developer guardrail for future producers feeding this sink - coordinate-only is already enforced at the command layer and via BamWithIndex sink-spec construction, so no runtime behavior changes.
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Replaces the arena chain sort sink's post-pass BAI re-read (
IndexBamFinalizeHook→noodles::bam::fs::index) with an inline indexer built during the BGZF write: per-record alignment context and per-physical-block compressed sizes are extracted in the parallelBgzfCompressstep, ride on eachBgzfBlockas a manifest, and are joined into aBaiBuilderowned by the serialWriteBgzfFile, which writes the.baiafter the BGZF EOF. No re-read, no new thread or channel, and zero overhead on the non-indexed path.Correctness is proven by samtools equivalence on the same BAM: the inline
.baimatchessamtools indexon region-query records andidxstatsacross placed, placed-but-unmapped, and truly-unplaced reads over multiple references, plus a multi-block case with a record that straddles a physical BGZF block. The 65280-byte block-stride identity between the compressor and the index resolver is relied on explicitly.This is the first PR of the sort→chain campaign. It does not route the
fgumi sortcommand onto the chain — the inline indexer is exercised chain-directly viaSinkSpec::BamWithIndex; the CLI cutover (and its wall-clock perf gate) follows in the next stacked PR.Suggested reading order
feat(bam-io): make extract_alignment_context public and namedfeat(bam-io): BaiBuilder record_with_context, prune_below, pub pendingfeat(pipeline-io): add BamIndexManifest sidecar to BgzfBlockfeat(pipeline): derive BAM index manifest in BgzfCompressfeat(pipeline-io): inline BAI indexing in WriteBgzfFilefeat(chains): inline BAI on the arena sink; drop re-read hooktest(chains): samtools-equivalence and byte-identity gate for the inline BAI arena sinkdocs(pipeline-io): note coordinate-order precondition on inline BAI indexerRisk: sort BAM output remains unchanged; the new
.baiis pinned byBamIndexManifestoffsets andsamtoolsequivalence tests;unsafe: none, with noCLAUDE.mdupdate; memory: adds bounded manifest storage with pruning, but changes no queue capacity, thread, or backpressure policy.WriteBgzfFileoutput.