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feat(fastq): run BAM→FASTQ on the typed-step chain and add paired split output - #939
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Priority: ➖ Normal Estimated code review effort: 4 (Complex) | ~45 minutes Change: Feature Sequence Diagram(s)sequenceDiagram
participant Fastq
participant TypedPipeline
participant PairedSplitSinks
participant FastqOutputs
Fastq->>TypedPipeline: configure UMI annotation and compression
TypedPipeline->>PairedSplitSinks: route R1, R2, and other reads
PairedSplitSinks->>FastqOutputs: write FASTQ or BGZF output
Merge Risk: ⚪ Minimal · up to The incremental test changes add coverage for the intended FASTQ behavior without exposing a concrete merge-blocking risk. 🚥 Pre-merge checks | ✅ 3✅ Passed checks (3 passed)
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Additional details and impacted files@@ Coverage Diff @@
## main #939 +/- ##
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+ Coverage 94.08% 94.52% +0.44%
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Lines 151854 151264 -590
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+ Hits 142868 142980 +112
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Inline comments:
In `@src/lib/commands/fastq.rs`:
- Around line 382-385: Update the paired-mode output collection around
SinkSpec::FastqPaired so the implicit stdout target for the default --out0 is
added to outputs when --out0 is omitted, allowing reject_output_collisions to
reject conflicts with --out1 - while preserving explicit --out0 handling.
In `@tests/integration/test_fastq_command.rs`:
- Around line 932-936: Strengthen the output comparison in the test around the
bwa-chunk-size assertion by reading the with_k output into a named byte buffer,
asserting it is non-empty, then comparing it with the without_k output. Preserve
the existing equality check and message while preventing both empty outputs from
passing.
- Around line 560-575: Add a paired-split coverage case using
create_bam_with_records with an empty sequence and quality, such as the PAIRED |
FIRST_SEGMENT flags and no RX tag, then assert the emitted four-line FASTQ
record round-trips as `@empty`\n\n+\n\n. Ensure the assertion exercises the
fan-out and per-branch writer paths.
- Around line 785-786: Strengthen the clap constraint tests using
Fastq::try_parse_from: in tests/integration/test_fastq_command.rs lines 785-786,
assert the error kind is MissingRequiredArgument for --out1 without --out2; in
lines 792-795, assert the error kind is ArgumentConflict for --output combined
with --out1/--out2, rather than checking only is_err().
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Inline comments:
In `@tests/integration/test_fastq_command.rs`:
- Around line 935-938: Update the doc comment above the paired split test to
remove the unsupported --require-flags claim, or add a test case that explicitly
passes -f; ensure the documented behavior matches the flags actually exercised
by the test.
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Inline comments:
In `@tests/integration/test_fastq_command.rs`:
- Around line 758-760: Bind the R2 compressed output path in the test instead of
constructing it only inline, then add assertions alongside the existing R1
checks that its bytes begin with gzip magic and end with fgumi_bgzf::BGZF_EOF.
Keep the existing R2 content assertions unchanged.
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Inline comments:
In `@tests/integration/test_fastq_command.rs`:
- Around line 919-920: Strengthen the collision tests around the execute failure
to verify the “before any write” contract: after each identical -1/-2 path
rejection, assert that the sink path was not created. Apply this to both
collision cases, preserving the existing error assertions and using the relevant
output-path variables.
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Inline comments:
In `@tests/integration/test_fastq_command.rs`:
- Around line 957-960: Extend the paired FASTQ integration tests around the
existing output-alias cases to cover --out1, --out2, and optional --out0
colliding with --input via direct paths and symlinks. Run each case with the
input file present, assert the expected validation error before sink execution,
and verify the input size is unchanged afterward.
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Inline comments:
In `@tests/integration/test_fastq_command.rs`:
- Around line 795-796: Extend the paired compression test around the existing
gz_r1/gz_r2 setup to run outputs with mixed-case and BGZF suffixes such as .bgzf
and .BGZ. Reuse the existing gzip-magic, BGZF_EOF, and decompressed-content
assertions so these suffixes are verified as BGZF-compressed outputs rather than
plain text.
- Around line 684-685: Replace the affected empty-output assertions around
test_fastq_paired_split_emits_degenerate_empty_record and both flag-filter cases
with fs::read_to_string byte-emptiness checks, rather than
parse_fastq_records(...).is_empty(). Apply this to R2, out0, and rf0 while
preserving the existing assertion messages and expected empty-file behavior.
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Inline comments:
In `@tests/integration/test_fastq_command.rs`:
- Around line 679-683: Strengthen the degenerate R1 assertion in the test around
parse_fastq_records to verify the exact four-line byte representation
`@empty`\n\n+\n\n, rather than relying only on the parsed tuple. Match the
byte-level oracle used by the sibling assertions and preserve the documented
empty-sequence record contract.
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Inline comments:
In `@tests/integration/test_fastq_command.rs`:
- Around line 1057-1059: Add collision coverage for --out0 against -1 by adding
a test case using -1 <p>, -2 <q>, and -0 <p>; reuse the existing error-content
and sink non-existence assertions to verify rejection occurs before any output
is opened.
- Around line 598-599: Update the ambiguous-read integration test around the
existing solo record to add a record with PAIRED, FIRST_SEGMENT, and
LAST_SEGMENT flags, using the proposed both-read name and sequence/quality
values, and extend the rec0 expectation so it verifies routing to --out0. Keep
the existing single-end case unchanged.
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…it output Route `fgumi fastq` through the declarative chain like every other command, retiring the standalone reader loop, and add paired split output (`--out1`/`--out2`, optional `--out0`) mirroring `samtools fastq -1/-2/-0`. `execute()` now builds a `ChainSpec` (`SourceSpec::Bam` → `Stage::Fastq` → `SinkSpec::Fastq`/`FastqPaired`) and runs it via `build_for(spec).run()`, so the per-file BGZF writers share one work-stealing pool instead of the old loop's single-threaded conversion. The legacy `run_with_writer`/`write_to_stdout` methods and the ad-hoc `BgzfFastqWriter` are removed; the paired chain wiring (`SinkSpec::FastqPaired`, the 3-way encode step, `Process3`, `WriteRawFile`) was already present but had no production constructor until now. Paired split routes R1→`--out1`, R2→`--out2`, and single-end/ambiguous reads→ `--out0` (or stdout when omitted), omitting the `/1` `/2` suffix as samtools does. clap enforces `--out1`/`--out2` together and mutually exclusive with `--output`. Also: - Reuse the shared `reject_output_collisions` helper (as clip/codec do) for output-vs-output collisions — stdout multiplexing, `/dev/null`, and `./`/symlink aliases — plus a `reject_write_aliasing_input` guard mirroring `retag`/`copy_umi` for the output-vs-input clobber. - `path_is_gzip` becomes the single live gzip detector — case-insensitive, matching gz/bgz/bgzf — resolving the dormant-vs-live divergence noted in-tree. - `--bwa-chunk-size` is deprecated and ignored (the pipeline manages batching); queue memory defaults to a lean fixed 256 MiB total (derived from `QueueMemoryOptions::default()`) so RSS stays flat as `--threads` scales. - The old interleaved R1/R2-desync warning (FASTQ3-02) is dropped with the loop, as it was in the source change; the chain interleaved encode does not track it. Output is byte-identical to `samtools fastq` (interleaved and `-1/-2/-0`, including reverse-complemented mates) and valid BGZF for `.gz` paths.
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Ports the
fgumi fastqchanges from #482 onto currentmain.fgumi fastqwas the last command still running on a standalone reader loop; every other command already runs on the declarative typed-step chain, and the paired-split chain wiring #482 introduced (SinkSpec::FastqPaired, the 3-way encode step,Process3,WriteRawFile) has been sitting onmainwith no production constructor. This wires it up.What's here
execute()now builds aChainSpec(SourceSpec::Bam→Stage::Fastq→SinkSpec::Fastq/FastqPaired) and runs it throughbuild_for(spec).run()for both output shapes, so the per-file BGZF writers share one work-stealing pool. The legacyrun_with_writer/write_to_stdoutloop and the ad-hocBgzfFastqWriterare retired.--out1/-1,--out2/-2, optional--out0/-0) mirrorssamtools fastq -1/-2/-0: R1 →--out1, R2 →--out2, single-end/ambiguous →--out0(or stdout when omitted), with the/1/2suffix omitted (the file identifies the mate). clap enforces--out1/--out2together and mutually exclusive with--output.reject_output_collisionshelper (shared with clip/codec — handles stdout multiplexing,/dev/null, and.//symlink aliases) plus areject_write_aliasing_inputcheck mirroringretag/copy_umi.path_is_gzipis now the single, case-insensitivegz/bgz/bgzfdetector, resolving the dormant-vs-live divergence noted in-tree.--bwa-chunk-sizeis deprecated and ignored (the pipeline manages batching); a non-default value logs a notice. Queue memory defaults to a lean fixed 256 MiB total (derived fromQueueMemoryOptions::default()) so RSS stays flat as--threadsscales.Behavior changes worth calling out
--out1/--out2) when mates may be missing..bgzfinterleaved output path (-o out.bgzf) is now written as BGZF rather than plain text under a.bgzfname (the old detector matched onlygz/bgz). This is a fix.Validation
samtools fastqfor interleaved,-1/-2/-0, reverse-complement R2, and.gz(decompressed); empty-input completes without hanging; all error guards exercised.cargo ci-fmt/cargo ci-lintclean; full suite green.-K/alias coverage and a stronger.gzoracle).Relates to #480 / #482.
Risk:
fgumi fastqoutput changes for interleaved and paired-split routing, pinned by typed-step routing and integration tests; grouping, consensus, sort order, corrected UMIs, and metrics are none;unsafechanges are none, and theCLAUDE.mdallowlist is unchanged; queue memory uses a fixed 256 MiB default with shared work-stealing backpressure. Fix: use the typed-step chain with validation guards and integration tests.--out1,--out2, and optional--out0.gz,bgz, andbgzfsuffixes case-insensitively.--bwa-chunk-size.