Add real-world fixtures for 11 previously-uncovered formats - #37
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Extend the license-vetted real fixture suite from 5 covered validated formats to 16, so nearly every hand-written validator now runs against canonical tool/portal output offline. New Tier-1 coverage (validated formats that previously had no real fixture): SAM, FASTA, FASTQ, PAF, BEDPE, narrowPeak, broadPeak, bedGraph, WIG, and Picard interval_list. Plus one Tier-2 depth item: a real BED12 (IsoSeq collapsed transcripts) exercising the block fields (thickStart/thickEnd, itemRgb, blockCount/blockSizes/blockStarts) that the existing 3-column BED fixture never touched. Sources are all redistribution-safe: samtools examples (MIT), the nf-core/test-datasets modules branch (MIT), and the Ensembl sample WIG (Apache-2.0, the canonical UCSC wiggle example covering BED-style, variableStep and fixedStep in one file). All 11 fixtures pass the existing offline contract, including the zero-diagnostic guard: unlike the GENCODE round, no validator false positives surfaced -- the newly-covered validators already handle canonical input cleanly.
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Summary
Extends the license-vetted real-world fixture suite (added in #35) from 5 covered validated formats to 16. Nearly every hand-written validator now runs against canonical tool/portal output in the offline verify suite.
The prior GENCODE round proved the value of this: real data immediately caught three validator false positives (#36). This round does the same for the formats that had never seen real input.
New coverage
Tier 1 — validated formats with zero prior fixtures:
examples/toy.samexamples/toy.faTier 2 — depth on an already-covered format:
thickStart/thickEnd,itemRgb, andblockCount/blockSizes/blockStarts. The only prior BED fixture was 3-column, so the block fields had never seen real input.The WIG fixture is particularly good value: one file covering BED-style,
variableStep, andfixedStepsections.Result
All 11 new fixtures pass the existing offline contract (pinned sha256, supported-format, validates-without-throwing, min-rows) including the zero-diagnostic guard. Unlike the GENCODE round, no validator false positives surfaced — the newly-covered validators already handle canonical input cleanly. Each was separately smoke-tested to confirm it is live (emits on malformed input), so the clean result is meaningful rather than a no-op.
Not in scope (follow-ups)
getValidatorreturns nothing, so they can't join this harness until they have a validator. That's a separate "should we validate these?" decision.start=without a numeric check; the interval_list declarative spec enforces min-columns + strand only). These are false-negatives on synthetic input, not false positives, so they don't affect any fixture — noting for a possible validator-hardening pass.