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feat(metrics)!: publish metric column manifest; headered filter --stats - #979
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Included review availability: 1 review is currently available. Your included PR review attempts over the past 7 days set your current allowance at 2 reviews per hour. WalkthroughMetric output now uses shared serialization paths. Filter statistics use a headered, one-row TSV format. The change adds a metric-column manifest and tests for serialization, writer behavior, and output contracts. ChangesMetric output and validation
Estimated code review effort: 4 (Complex) | ~45 minutes Sequence Diagram(s)sequenceDiagram
participant FilterCommand
participant FilterStatsMetrics
participant MetricsWriter
FilterCommand->>FilterStatsMetrics: Build stats row from counts
FilterCommand->>MetricsWriter: Write row as metrics TSV
MetricsWriter-->>FilterCommand: Return write result
Suggested labels: Merge Risk: ⚪ Minimal · up to Metric outputs now go through one shared writer, which handles gzip, symlinks, stdout and descriptor destinations, and empty-result headers. The earlier concerns about overwriting symlinks, clobbering redirected stdout, unsafe temp files, missing fsync, and appending to files under 🚥 Pre-merge checks | ✅ 3✅ Passed checks (3 passed)
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In `@crates/fgumi-metrics/src/writer.rs`:
- Around line 128-137: Update resolve_symlink to preserve dangling symlinks:
after canonicalize fails, use read_link to obtain the target, joining relative
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In `@crates/fgumi-metrics/src/writer.rs`:
- Around line 87-90: Update the writer’s early in-place-write check before
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In `@crates/fgumi-metrics/src/writer.rs`:
- Line 99: Update the `Builder::make_in` closure in the temporary-file creation
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In `@crates/fgumi-metrics/src/writer.rs`:
- Around line 100-101: In the metrics writer, call sync_all on the temporary
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BREAKING CHANGE: `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.
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.
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Inline comments:
In `@crates/fgumi-metrics/src/writer.rs`:
- Around line 179-184: Narrow is_kernel_special_path to recognize only
descriptor aliases (/dev/stdout, /dev/stderr, /dev/stdin, /dev/fd/*, and
/proc/*/fd/*), rather than every path under /dev or /proc. Leave real devices
and FIFOs to is_non_regular_file, so regular files such as those under /dev/shm
still use the atomic replacement path in write_metrics_atomic. Add a Linux test
that writes twice to a regular file under a non-descriptor /dev path and
verifies it contains only one header.
In `@src/lib/commands/review.rs`:
- Around line 1144-1156: Replace the separate empty and nonempty TSV-writing
branches near ConsensusVariantReviewInfo::tsv_header with the shared atomic
metrics writer for the complete all_metrics collection, preserving the review
output format and allowing empty results to produce the appropriate header-only
file.
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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.
…te_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.
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Real fgumi 0.7.0+ outputs (fulcrumgenomics/fgumi#979) generated from simulated reads: group, simplex/duplex (--stats and simplex-/duplex-metrics), dedup, correct, filter, clip, retag, copy-umi and downsample metrics.
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Summary of changes
This makes every fgumi metric output a well-formed, fgbio-style
MetricTSV and publishes the column contract, as groundwork for reading all fgumi metrics in MultiQC.Breaking:
filter --statsis now a headered one-row metrics TSV.key<TAB>valuefile.total_reads / passed_reads / failed_reads / pass_rateheader row plus one data row, written through the shared metrics writer via a newFilterStatsMetricsstruct.pass_rateis now full precision rather than rounded to 4 decimals.Column manifest:
crates/fgumi-metrics/metric_columns.json. This lists the ordered columns of all 23 metric files fgumi emits, keyed<namespace>.<file>, becausegroup,simplex,duplexanddedupeach write a differently shaped*.family_sizes.txt.tests/integration/test_metric_contract.rsparses the workspace withsynand fails in three cases:Serializeis neither listed nor allowlisted with a reason;f64field lackscrate::float, so non-finite values would be written asinf, which fgbio'sMetric.readrejects, instead ofInfinity/NaN.Metrics-writer fixes. These apply to every output that goes through
write_metrics:.gzpath is now actually gzip-compressed. Before, it was plain text under a.gzname that fgumi's own reader could not read back./dev/stdout, FIFOs and>(...)are written in place. Before, they failed at rename time, after the whole run.Empty outputs keep their header. These used to write a 0-byte file, which fgbio rejects with "No header found":
group --family-size-histogramgroup --metricsfamily- and position-group-size histogramsdedup --family-size-histogramand--duplication-ladderdownsample --histogram-kept/--histogram-rejectednow serialize aDownsampleHistogramMetricthrough the shared writer instead of hand-formattedwriteln!. The output is byte-identical, pinned by an exact-bytes test.Tests:
Someoptions.--statslayout are updated.Issue(s) addressed by this PR
There is no tracking issue. This is the first step toward MultiQC support for all fgumi metrics; a follow-up will add the MultiQC module, which pins its schemas to
metric_columns.json.Reviewer guidance
Suggested reading order:
crates/fgumi-metrics/src/filter_stats.rs, thensrc/lib/pipeline/chains/commands/filter.rs(the format change).crates/fgumi-metrics/src/writer.rs(destination handling:write_metrics_atomic,write_metrics_to,is_non_regular_file,resolve_symlink).tests/integration/test_metric_contract.rstogether withmetric_columns.json.src/lib/commands/{group,dedup,downsample}.rs.Notes:
ConsensusMetricsis allowlisted in the completeness check. It is a counter struct projected into theconsensus.statskey/value rows, not written as its own file.ConsensusKvMetricdeliberately does not implementMetric; it is always written non-empty.test_filter_cutover_parity.rs, theFGUMI_BASELINE_BINbranch now compares--statsby value, not byte-for-byte, because a pre-change baseline writes the old layout. Counts are compared exactly, andpass_ratewithin the old 4-decimal rounding. I verified this against a pre-change release binary: it fails before the fix and passes after.Does this introduce a breaking change?
fgumi filter --statschanges layout from a headerless two-column key/value file to a headered one-row TSV. Column names and semantics are unchanged;pass_rateis now full precision. Parsers of the old layout must read it as a normal headered TSV, for examplepd.read_csv(path, sep="\t"). The squash commit should carry the!and aBREAKING CHANGE:footer. There is also a hand-written[Unreleased]CHANGELOG entry.✔️ Checklist
cargo ci-fmt,cargo ci-lint,cargo ci-test(plus the filter cutover-parity tests withFGUMI_BASELINE_BINset)README.mdanddocs/*)Risk verdict: Metrics output changes for
filter --statsand empty histograms; the column manifest and serialization tests pin the format. Nounsafechanges; the CLAUDE.md allowlist needs no update. No memory-bound, queue-capacity, or thread/backpressure changes.Fix: Write
filter --statsas a headered, one-row TSV and update consumers to parse it.The shared metrics writer preserves headers for empty outputs and handles gzip paths, special files, and symlink destinations. Downsample, deduplication, and grouping histograms use the shared writer.
Integration tests check the manifest against serialized metric types and validate float encoding. Test-run results were not provided.