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feat(compare): harden fgumi compare into a sound, faithful fgbio-parity oracle - #530

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nh13 merged 39 commits into

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nh/compare-hardening

Jul 19, 2026

Commits on Jul 18, 2026

feat(compare): RecordKey identity and content-predicate primitives
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9b80300
feat(compare): positional comparison engine (key-lockstep, no resync)
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e5654a1
feat(compare): group key-join engine (queryname canonicalize + MI bijection)
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89d2f88
feat(compare): sort-order verification engine (by sort-key, tie-tolerant)
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34ecb75
feat(compare): BAM header comparison (@HD/@SQ/@RG; normalize @PG/@CO)
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061f5cd
feat(compare): metrics comparison by row key-join (localized, faithful)
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6163671
feat(compare): wire presets onto the engines; reuse sort tmp-dir env; docs
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4f9901c
test(compare): mutation/metamorphic soundness harness and integration tests
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53db25c
fix(compare): reject duplicate metric keys instead of multiset-matching them
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f37db5b
fix(compare): compare consensus depth tags exactly (drop the saturation carve-out)
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d411e3c
fix(compare)!: make Content the sound default; remove reorder-unsound Full
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f0f8e80
refactor(compare): consolidate ExactConsensus into Exact
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d049e1f
test(compare): assert exact exit code in metrics subprocess tests
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1e6b6ff
test(compare): make the multi-column metrics key test load-bearing
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ea4244d
test(compare): rstest + proptest for record_keys_match equivalence
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f684b8b
docs(compare): correct the --sort-tmp-dir default description
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c1f917b
feat(compare): semantic sort-order header precondition (fgumi/fgbio SS spellings)
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3a1b428
feat(compare): hard-exit on incompatible headers; decide SS semantically
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d5c7fb8
feat(compare): verify records are in the declared sort order (universal precondition)
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c501040
docs(compare): cross-reference the two SortOrder dispatch sites
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20d4a56
feat(compare): per-molecule run iterator with MI-invariant canonical id
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2456b38
feat(compare): per-molecule membership/content/strand comparison
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3e33688
feat(compare): two-sided streaming molecule hash-join driver
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7e63acb
refactor(compare)!: grouping via streaming molecule-join; drop external sort + keyjoin
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eba73a0
feat(compare): guard MI-less grouping input; molecule-join coverage
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9a65f9e
fix(compare): exempt empty inputs from the MI-less grouping guard
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2ee54a8
test(compare): assert grouping molecule-join never spills to disk
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9c83131
fix(compare): make molecule-join verdict independent of --max-diffs cap
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d6f4620
test(compare): pin balanced-residual verdict at --max-diffs 0
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268c30c

Commits

Commits on Jul 18, 2026

Commits on Jul 19, 2026