P3-15′-c-ii: the criterion (c) synteny predicate, its per-candidate producer, and D4's two symmetric diagnostics by bioedca · Pull Request #114 · bioedca/tbox-finder

feat(mining): P3-15'-c-ii — the criterion (c) synteny predicate, its per-candidate producer, and D4's two symmetric diagnostics

bioedcam

committed

ba04aea

fix(mining): P3-15'-c-ii review round 1 — the tandem carve-out now reaches the decision, not just the search

bioedcam

committed

4b49352

fix(mining): P3-15'-c-ii review round 2 — the 5'UTR false-pass arm contained its own positive class

bioedcam

committed

b61fd3a

fix(mining): P3-15'-c-ii review round 3 — a filtered subset that outnumbered its source

bioedcam

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c7beb0a

fix(mining): P3-15'-c-ii review round 4 — "the same windows, filtered" was still not true

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b6234ec

test(mining): P3-15'-c-ii review round 5 — assert object identity, not tuple equality

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b9aefb4

fix(mining): P3-15'-c-ii review round 6 — the sub-threshold test used a genomic span, not a coding length

bioedcam

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1f9e3ab

fix(mining): P3-15'-c-ii review round 7 — ProducerError was not the failure surface

bioedcam

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3991fa2

fix(mining): P3-15'-c-ii review round 8 — duplicate-key collapse on the READ path, and a fifth vacuous test

bioedcam

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a5b1fd0

fix(mining): P3-15'-c-ii review round 9 — the false-pass rate divided by windows the rule was never asked about

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cd3c01d

fix(mining): P3-15'-c-ii review round 10 — the positive control published a PASS rate under a false_pass_rate key

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2f9563d

fix(mining): P3-15'-c-ii review round 11 — a bare gene symbol suppressed the symbol route it would have fed

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bd493ba

fix(mining): P3-15'-c-ii review round 12 — one bad GFF among 339 would have aborted all 941 verdicts

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24fa382

fix(mining): P3-15'-c-ii review round 13 — round 11's guard keyed on the wrong thing and would have discarded what it protected

bioedcam

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9069d95

test(mining): P3-15'-c-ii review round 14 — a one-class assertion guarding a four-class risk

bioedcam

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ee9108c

fix(mining): P3-15'-c-ii review round 15 — a required parameter that nothing read, and two reports that could land out of step

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65f64af

fix(mining): P3-15'-c-ii review round 16 — round 12 guarded one of two sibling reads

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9b7a4e9

docs(dev-log): correct the round-16 pass count — 4,683, not 4,687

bioedcam

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14a66b7

fix(mining): P3-15'-c-ii review round 17 — strided sharding defeated the cache the module is built around

bioedcam

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bb76e3a

docs(dev-log): add the round-17 stanza dropped by a short-circuited compound

bioedcam

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231ffde

test(mining): P3-15'-c-ii review round 18 — three instances of "fixed one of two identical things"

bioedcam

committed

3cf5e7b

docs(dev-log): P3-15'-c-ii review round 19 — no new findings, the gate is met

bioedcam

committed

be43605

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P3-15′-c-ii: the criterion (c) synteny predicate, its per-candidate producer, and D4's two symmetric diagnostics - #114

P3-15′-c-ii: the criterion (c) synteny predicate, its per-candidate producer, and D4's two symmetric diagnostics#114
bioedca merged 22 commits into
mainfrom
p3-15c-ii-synteny

Commits on Aug 7, 2026

feat(mining): P3-15'-c-ii — the criterion (c) synteny predicate, its per-candidate producer, and D4's two symmetric diagnostics

fix(mining): P3-15'-c-ii review round 1 — the tandem carve-out now reaches the decision, not just the search

fix(mining): P3-15'-c-ii review round 2 — the 5'UTR false-pass arm contained its own positive class

fix(mining): P3-15'-c-ii review round 3 — a filtered subset that outnumbered its source

fix(mining): P3-15'-c-ii review round 4 — "the same windows, filtered" was still not true

test(mining): P3-15'-c-ii review round 5 — assert object identity, not tuple equality

fix(mining): P3-15'-c-ii review round 6 — the sub-threshold test used a genomic span, not a coding length

fix(mining): P3-15'-c-ii review round 7 — ProducerError was not the failure surface

fix(mining): P3-15'-c-ii review round 8 — duplicate-key collapse on the READ path, and a fifth vacuous test

fix(mining): P3-15'-c-ii review round 9 — the false-pass rate divided by windows the rule was never asked about

fix(mining): P3-15'-c-ii review round 10 — the positive control published a PASS rate under a false_pass_rate key

fix(mining): P3-15'-c-ii review round 11 — a bare gene symbol suppressed the symbol route it would have fed

fix(mining): P3-15'-c-ii review round 12 — one bad GFF among 339 would have aborted all 941 verdicts

fix(mining): P3-15'-c-ii review round 13 — round 11's guard keyed on the wrong thing and would have discarded what it protected

test(mining): P3-15'-c-ii review round 14 — a one-class assertion guarding a four-class risk

fix(mining): P3-15'-c-ii review round 15 — a required parameter that nothing read, and two reports that could land out of step

fix(mining): P3-15'-c-ii review round 16 — round 12 guarded one of two sibling reads

docs(dev-log): correct the round-16 pass count — 4,683, not 4,687

fix(mining): P3-15'-c-ii review round 17 — strided sharding defeated the cache the module is built around

docs(dev-log): add the round-17 stanza dropped by a short-circuited compound

test(mining): P3-15'-c-ii review round 18 — three instances of "fixed one of two identical things"

docs(dev-log): P3-15'-c-ii review round 19 — no new findings, the gate is met