{ "about": { "method": "exact-fragment-search (src/lib/seq/fragment-search.ts)", "generatedBy": "pipeline/sequence-toolkit/exact_matches.py", "recordedOn": "2026-10-10", "oracle": "An independent Python derivation; reverse complements by Biopython 1.88 (Bio.Seq.reverse_complement), every site and hit found by testing each window directly", "conventions": [ "Query: line breaks and spaces are removed and letters upper-cased; nothing else is removed. Refusals in this order: a raw query over 20,000 characters is long; an empty one is empty; any letter other than A, C, G, T is alphabet (no ambiguity codes, no U); under 4 bases is short; over 10,000 bases is long.", "The saved sequence is read on its saved, presented strand. Its letters must be A, C, G, T or the IUPAC DNA codes R Y S W K M B D H V N; any other letter refuses the search (residues). An IUPAC code in the saved sequence is a literal letter that no query base equals, never a wildcard.", "A hit is a window equal to the query ('+') or to its reverse complement ('-'); when the query is its own reverse complement a window is reported once, as 'both'. Overlapping hits are all kept.", "Coordinates are 1-based and inclusive on the saved strand; start is the window's first base and end its last, whatever the strand. On a circular molecule each of the n start positions is read once and a hit that crosses the origin has wraps true (end < start, or a full-length query); on a linear one no hit wraps. A query longer than the molecule has no hit.", "Hits are listed by start, then by strand ('+', '-', 'both')." ], "inputs": "A long input is stored as {\"parts\": [[unit, times], ...]}, the units concatenated in order.", "ruling": "CSO, 10 October 2026 (docs/board/memos/2026-10-10-cso-wave2-cloning.md ยง2.4): independent, published, hashed; never generated by the engine under test." }, "cases": [ { "id": "frag-forward", "note": "One forward hit on a linear sequence.", "input": { "residues": "TTAACCGTGGCATG", "query": "AACCGT", "circular": false }, "expected": { "ok": true, "query": "AACCGT", "matches": [ { "start": 3, "end": 8, "wraps": false, "strand": "+" } ] } }, { "id": "frag-reverse", "note": "One hit of the reverse complement, reported on the saved strand's coordinates.", "input": { "residues": "GGACGGTTAACATG", "query": "AACCGT", "circular": false }, "expected": { "ok": true, "query": "AACCGT", "matches": [ { "start": 3, "end": 8, "wraps": false, "strand": "-" } ] } }, { "id": "frag-palindrome-once", "note": "A palindromic query (GAATTC) is reported once per site as 'both', never twice.", "input": { "residues": "CCGAATTCAAGAATTCGG", "query": "GAATTC", "circular": false }, "expected": { "ok": true, "query": "GAATTC", "matches": [ { "start": 3, "end": 8, "wraps": false, "strand": "both" }, { "start": 11, "end": 16, "wraps": false, "strand": "both" } ] } }, { "id": "frag-homopolymer-overlaps", "note": "Overlapping hits in a homopolymer are all kept.", "input": { "residues": "CAAAAAAAC", "query": "AAAA", "circular": false }, "expected": { "ok": true, "query": "AAAA", "matches": [ { "start": 2, "end": 5, "wraps": false, "strand": "+" }, { "start": 3, "end": 6, "wraps": false, "strand": "+" }, { "start": 4, "end": 7, "wraps": false, "strand": "+" }, { "start": 5, "end": 8, "wraps": false, "strand": "+" } ] } }, { "id": "frag-homopolymer-reverse", "note": "A homopolymer of T read with an A query: overlapping hits on the reverse strand only.", "input": { "residues": "GTTTTTTG", "query": "AAAA", "circular": false }, "expected": { "ok": true, "query": "AAAA", "matches": [ { "start": 2, "end": 5, "wraps": false, "strand": "-" }, { "start": 3, "end": 6, "wraps": false, "strand": "-" }, { "start": 4, "end": 7, "wraps": false, "strand": "-" } ] } }, { "id": "frag-tandem-repeat", "note": "A tandem repeat: every repeat unit and every overlapping placement is a hit.", "input": { "residues": "ACGTTACGTTACGTTACG", "query": "ACGTTACG", "circular": false }, "expected": { "ok": true, "query": "ACGTTACG", "matches": [ { "start": 1, "end": 8, "wraps": false, "strand": "+" }, { "start": 6, "end": 13, "wraps": false, "strand": "+" }, { "start": 11, "end": 18, "wraps": false, "strand": "+" } ] } }, { "id": "frag-iupac-barrier", "note": "N in the saved sequence is a literal letter, never a wildcard: only the clean copy is found.", "input": { "residues": "AANNNAACCGTNNAACNGT", "query": "AACCGT", "circular": false }, "expected": { "ok": true, "query": "AACCGT", "matches": [ { "start": 6, "end": 11, "wraps": false, "strand": "+" } ] } }, { "id": "frag-iupac-codes", "note": "Every IUPAC code in the saved sequence blocks a match through it.", "input": { "residues": "AACRGTAACYGTAACSGTAACCGT", "query": "AACCGT", "circular": false }, "expected": { "ok": true, "query": "AACCGT", "matches": [ { "start": 19, "end": 24, "wraps": false, "strand": "+" } ] } }, { "id": "frag-linear-no-wrap", "note": "On a linear molecule a query across the end is not found.", "input": { "residues": "CCGTGGAA", "query": "AACCGT", "circular": false }, "expected": { "ok": true, "query": "AACCGT", "matches": [] } }, { "id": "frag-circular-origin", "note": "On a circular molecule the same query spans the origin.", "input": { "residues": "CCGTGGAA", "query": "AACCGT", "circular": true }, "expected": { "ok": true, "query": "AACCGT", "matches": [ { "start": 7, "end": 4, "wraps": true, "strand": "+" } ] } }, { "id": "frag-circular-origin-reverse", "note": "A reverse-strand hit across the origin of a circular molecule.", "input": { "residues": "GGTTCCAC", "query": "AACCGT", "circular": true }, "expected": { "ok": true, "query": "AACCGT", "matches": [ { "start": 7, "end": 4, "wraps": true, "strand": "-" } ] } }, { "id": "frag-circular-full-length", "note": "A query as long as the circular molecule is found at each start where it reads, wrapping.", "input": { "residues": "AACCTTGG", "query": "CCTTGGAA", "circular": true }, "expected": { "ok": true, "query": "CCTTGGAA", "matches": [ { "start": 3, "end": 2, "wraps": true, "strand": "+" } ] } }, { "id": "frag-circular-homopolymer", "note": "A homopolymer circle: every start is a hit, read once.", "input": { "residues": "AAAA", "query": "AAAA", "circular": true }, "expected": { "ok": true, "query": "AAAA", "matches": [ { "start": 1, "end": 4, "wraps": false, "strand": "+" }, { "start": 2, "end": 1, "wraps": true, "strand": "+" }, { "start": 3, "end": 2, "wraps": true, "strand": "+" }, { "start": 4, "end": 3, "wraps": true, "strand": "+" } ] } }, { "id": "frag-query-longer", "note": "A query longer than the molecule has no hit, circular or not.", "input": { "residues": "AAAA", "query": "AAAAA", "circular": true }, "expected": { "ok": true, "query": "AAAAA", "matches": [] } }, { "id": "frag-mixed-strands", "note": "Hits on both strands, listed by start.", "input": { "residues": "AAGGCTTTAGCCTTAAGGC", "query": "AAGGC", "circular": false }, "expected": { "ok": true, "query": "AAGGC", "matches": [ { "start": 1, "end": 5, "wraps": false, "strand": "+" }, { "start": 10, "end": 14, "wraps": false, "strand": "-" }, { "start": 15, "end": 19, "wraps": false, "strand": "+" } ] } }, { "id": "frag-normalised-query", "note": "Lower case, spaces and line breaks in the query are read as the same bases.", "input": { "residues": "TTAACCGTGG", "query": "aac c\ngt", "circular": false }, "expected": { "ok": true, "query": "AACCGT", "matches": [ { "start": 3, "end": 8, "wraps": false, "strand": "+" } ] } }, { "id": "frag-refuse-empty", "note": "A query of spaces only refuses as empty.", "input": { "residues": "AACCGT", "query": " \n ", "circular": false }, "expected": { "ok": false, "reason": "empty" } }, { "id": "frag-refuse-short", "note": "Three bases refuse as short.", "input": { "residues": "AACCGT", "query": "AAC", "circular": false }, "expected": { "ok": false, "reason": "short" } }, { "id": "frag-refuse-alphabet-n", "note": "An ambiguity code in the query refuses: the query is never a pattern.", "input": { "residues": "AACCGT", "query": "AACN", "circular": false }, "expected": { "ok": false, "reason": "alphabet" } }, { "id": "frag-refuse-alphabet-u", "note": "U in the query refuses; RNA is not converted.", "input": { "residues": "AACCGT", "query": "AACU", "circular": false }, "expected": { "ok": false, "reason": "alphabet" } }, { "id": "frag-refuse-alphabet-header", "note": "A FASTA header in the query refuses; nothing is stripped but whitespace.", "input": { "residues": "AACCGT", "query": ">q\nAACCGT", "circular": false }, "expected": { "ok": false, "reason": "alphabet" } }, { "id": "frag-refuse-alphabet-before-short", "note": "A short query with a bad letter refuses as alphabet, the first check that fails.", "input": { "residues": "AACCGT", "query": "AAN", "circular": false }, "expected": { "ok": false, "reason": "alphabet" } }, { "id": "frag-refuse-long", "note": "10,001 bases refuse as long.", "input": { "residues": "AACCGT", "query": { "parts": [ [ "A", 10001 ] ] }, "circular": false }, "expected": { "ok": false, "reason": "long" } }, { "id": "frag-accept-max", "note": "10,000 bases are read (longer than the molecule: no hit).", "input": { "residues": "AACCGT", "query": { "parts": [ [ "A", 10000 ] ] }, "circular": false }, "expected": { "ok": true, "query": "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ", "matches": [] } }, { "id": "frag-refuse-raw-long", "note": "A raw query over 20,000 characters refuses as long before anything is removed.", "input": { "residues": "AACCGT", "query": { "parts": [ [ "A ", 10001 ] ] }, "circular": false }, "expected": { "ok": false, "reason": "long" } }, { "id": "frag-refuse-residues", "note": "A saved sequence with U refuses the search; it is not DNA on its saved strand.", "input": { "residues": "AACUGT", "query": "AACCGT", "circular": false }, "expected": { "ok": false, "reason": "residues" } } ] }