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obitools4/pkg/obiprimer/testdata/ecoprimers_Teleostei.words.tsv
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Eric Coissac ad065f6853 Introduce new sequence matching logic and corpus handling
This commit introduces the core matching functionality, including parallel corpus loading, the `Corpus` data structure, and implementations for `matchNaive` and `matchApat`. It also defines new matching rules, variant handling, and comprehensive unit and integration tests to validate the new logic and parameter handling.
2026-11-03 22:35:51 +11:00

6.5 KiB

1AAAACTCGTGCCAGCCAC38910
2AAACCCAAAGGACTTGGC38900
3AAACGAACCCTTAATAGC38750
4AAACTCGTGCCAGCCACC38940
5AAACTGGGATTAGATACC38960
6AAAGTCCTACGTGATCTG39010
7AAATCATGATGCAAAAGG38940
8AACAAACGAACCCTTAAT38880
9AACATCGAGGTCGTAAAC38930
10AACATGGTAAGTGTACCG38940
11AACCAAAAACTCTTGGTG38540
12AACCCAAAGGACTTGGCG38880
13AACCCTTAATAGCGGCTG38580
14AACCGCGGTGGCTGGCAC38960
15AACGAACCCTTAATAGCG38600
16AACGATTAAAGTCCTACG37000
17AACGTCAGGTCGAGGTGT38940
18AACTCAGATCACGTAGGA38990
19AACTCGTGCCAGCCACCG38930
20AACTGGGATTAGATACCC38960
21AAGAGTTTTTGGTTCCTA38480
22AAGCCTCGCCTGTTTACC38760
23AAGGGTTCGTTTGTTCAA38890
24AAGGTAGCGCAATCACTT38890
25AAGTCCTACGTGATCTGA39000
26AAGTCGTAACATGGTAAG38930
27AAGTGCACCTTCCGGTAC38880
28AAGTGTACCGGAAGGTGC38890
29AATAGCGGCTGCACCATT38390
30AATCACTTGTCTTTTAAA38560
31AATCATGATGCAAAAGGT38930
32AATCCAGGTCAGTTTCTA39030
33AATCGTTGAACAAACGAA38760
34AATGTAGCCCATTTCTTC38710
35ACAAACGAACCCTTAATA38850
36ACAAACTGGGATTAGATA38930
37ACAAGTGATTGCGCTACC38890
38ACACACCGCCCGTCACTC38910
39ACACCGCCCGTCACTCTC38900
40ACACTTACCATGTTACGA38930
41ACATCCTAATGGTGCAGC38580
42ACATCGAGGTCGTAAACC38940
43ACATGGTAAGTGTACCGG38940
44ACCAAAAACTCTTGGTGC38750
45ACCAAGAGTTTTTGGTTC38570
46ACCATGTTACGACTTGCC38910
47ACCATTAGGATGTCCTGA38910
48ACCCAAAGGACTTGGCGG38860
49ACCCGTCTCTGTGGCAAA38920
50ACCCTAGGGATAACAGCG38950
51ACCCTTAATAGCGGCTGC38610
52ACCGCCCGTCACTCTCCC38930
53ACCGCGGTGGCTGGCACG38950
54ACCGGAAGGTGCACTTGG38870
55ACCTCGATGTTGGATCAG38910
56ACCTTCCGGTACACTTAC38930
57ACGAACCCTTAATAGCGG38590
58ACGACCTCGATGTTGGAT38890
59ACGATTAAAGTCCTACGT37010
60ACGTCAGGTCGAGGTGTA38940
61ACGTGATCTGAGTTCAGA39010
62ACTCAGATCACGTAGGAC38990
63ACTCGTGCCAGCCACCGC38940
64ACTCTTTTGCCACAGAGA38670
65ACTGGGATTAGATACCCC38960
66ACTTACCATGTTACGACT38940
67ACTTTAATCGTTGAACAA38760
68AGAACAGGCTCCTCTAGG38930
69AGACAAGTGATTGCGCTA38830
70AGAGGAGCCTGTTCTAGA38760
71AGAGTGACGGGCGGTGTG38900
72AGAGTTTTTGGTTCCTAA38510
73AGATAGAAACTGACCTGG39000
74AGATCACGTAGGACTTTA39010
75AGCCGCTATTAAGGGTTC38560
76AGCCTCGCCTGTTTACCA38890
77AGCCTGTTCTAGAACCGA38710
78AGCGGCTGCACCATTAGG38460
79AGGAACCAAAAACTCTTG38420
80AGGACATCCTAATGGTGC38660
81AGGACTTTAATCGTTGAA36880
82AGGAGCCTGTTCTAGAAC38740
83AGGATGTCCTGATCCAAC38970
84AGGCAAGTCGTAACATGG38680
85AGGCGATGTTTTTGGTAA38940
86AGGGATAACAGCGCAATC38960
87AGGGGAGGCAAGTCGTAA38900
88AGGGGGTTTACGACCTCG38940
89AGGGTTCGTTTGTTCAAC38880
90AGGTAGCGCAATCACTTG38880
91AGTCCTACGTGATCTGAG39000
92AGTGGGGTATCTAATCCC38960
93AGTTACCCTAGGGATAAC38950
94AGTTTTTGGTTCCTAAGA38480
95ATAGAAACTGACCTGGAT39010
96ATAGCGGCTGCACCATTA38370
97ATAGTGGGGTATCTAATC38950
98ATCACGTAGGACTTTAAT38800
99ATCACTTGTCTTTTAAAT38560
100ATCAGGACATCCTAATGG38920
101ATCATGATGCAAAAGGTA38940
102ATCCTAATGGTGCAGCCG38520
103ATCGAGGTCGTAAACCCC38940
104ATCGGTTCTAGAACAGGC38620
105ATCGTTGAACAAACGAAC38770
106ATCTGAGTTCAGACCGGA39020
107ATGATGCAAAAGGTACGA38910
108ATGGTAAGTGTACCGGAA38950
109ATGGTGCAGCCGCTATTA38400
110ATGTAGCCCATTTCTTCC38710
111ATGTCCTGATCCAACATC38920
112ATGTTACGACTTGCCTCC38640
113ATGTTGGATCAGGACATC38930
114ATGTTTTTGGTAAACAGG38870
115ATTAGATACCCCACTATG38960
116ATTAGGATGTCCTGATCC38930
117ATTGCGCTGTTATCCCTA38960
118CAAAAACTCTTGGTGCAA38860
119CAAACGAACCCTTAATAG38820
120CAAACTGGGATTAGATAC38950
121CAACATCGAGGTCGTAAA38940
122CAACGATTAAAGTCCTAC36910
123CAAGTCGTAACATGGTAA38930
124CAAGTGCACCTTCCGGTA38880
125CACCATTAGGATGTCCTG38900
126CACCGCCCGTCACTCTCC38880
127CACCTTCCGGTACACTTA38910
128CACGTAGGACTTTAATCG37020
129CACTCTTTTGCCACAGAG38560
130CACTTACCATGTTACGAC38940
131CATCCTAATGGTGCAGCC38520
132CATCGAGGTCGTAAACCC38940
133CATGATGCAAAAGGTACG38900
134CATGGTAAGTGTACCGGA38940
135CATGTTACGACTTGCCTC38660
136CATTAGGATGTCCTGATC38930
137CCAAAAACTCTTGGTGCA38830
138CCAACATCGAGGTCGTAA38940
139CCAAGAGTTTTTGGTTCC38440
140CCACTCTTTTGCCACAGA38790
141CCCACTCTTTTGCCACAG38790
142CCCGTCTCTGTGGCAAAA38940
143CCCTAGGGATAACAGCGC38980
144CCCTTAATAGCGGCTGCA38530
145CCGCCCGTCACTCTCCCC38900
146CCGCGGTGGCTGGCACGA38950
147CCGGTAAAACTCGTGCCA38470
148CCGGTCTGAACTCAGATC39040
149CCGTCTCTGTGGCAAAAG38940
150CCTACGTGATCTGAGTTC38990
151CCTAGGGATAACAGCGCA38960
152CCTCGATGTTGGATCAGG38920
153CCTCGCCTGTTTACCAAA38920
154CCTGTTCTAGAACCGATA38620
155CCTTAATAGCGGCTGCAC38500
156CCTTCCGGTACACTTACC38930
157CGAACCCTTAATAGCGGC38550
158CGACCTCGATGTTGGATC38900
159CGACGGCGGTATATAGGC38900
160CGATGTTGGATCAGGACA38920
161CGATGTTTTTGGTAAACA38860
162CGCCTGTTTACCAAAAAC38890
163CGCGGTGGCTGGCACGAG38940
164CGCTTAGCTGTTAACTAA38640
165CGGTAAAACTCGTGCCAG38560
166CGGTCTGAACTCAGATCA39040
167CGGTTCTAGAACAGGCTC38730
168CGTAACATGGTAAGTGTA38920
169CGTCAGGTCGAGGTGTAG38930
170CGTCTCTGTGGCAAAAGA38910
171CGTGATCTGAGTTCAGAC39020
172CGTTGAACAAACGAACCC38870
173CGTTTGTTCAACGATTAA38770
174CTAAATCATGATGCAAAA38960
175CTAATGGTGCAGCCGCTA38400
176CTACGTGATCTGAGTTCA38990
177CTAGAACAGGCTCCTCTA38770
178CTAGAGGAGCCTGTTCTA38910
179CTAGGGATAACAGCGCAA38970
180CTCCGGTCTGAACTCAGA39030
181CTCGATGTTGGATCAGGA38920
182CTCGCCTGTTTACCAAAA38920
183CTCGTACCTTTTGCATCA38890
184CTCTTTTGCCACAGAGAC38690
185CTGAACTCAGATCACGTA39000
186CTGCACCATTAGGATGTC38610
187CTGGGATTAGATACCCCA38950
188CTGTTATCCCTAGGGTAA38970
189CTGTTTACCAAAAACATC38860
190CTTAATAGCGGCTGCACC38480
191CTTAGCTGTTAACTAAGA38780
192CTTAGGAACCAAAAACTC38470
193CTTAGTTAACAGCTAAGC38750
194CTTCCGGTACACTTACCA38910
195CTTGGATTTGCACCAAGA38990
196CTTTAATCGTTGAACAAA38760
197CTTTTGCATCATGATTTA38960
198GAACAAACGAACCCTTAA38900
199GAAGGAACTCGGCAAACA38890
200GACAAGTGATTGCGCTAC38890
201GACCTCGATGTTGGATCA38900
202GACTTTAATCGTTGAACA36860
203GAGGAGCCTGTTCTAGAA38760
204GAGGCGATGTTTTTGGTA38930
205GATAGAAACTGACCTGGA39000
206GATCACGTAGGACTTTAA39000
207GATTAAAGTCCTACGTGA37040
208GCAAGTCGTAACATGGTA38910
209GCATAGTGGGGTATCTAA38960
210GCCGGTAAAACTCGTGCC38270
211GCCTCGCCTGTTTACCAA38900
212GCCTGTTTACCAAAAACA38890
213GCGATGTTTTTGGTAAAC38880
214GCGCTTAGCTGTTAACTA38990
215GCGGCTGCACCATTAGGA38500
216GCTAAATCATGATGCAAA38930
217GCTACACCTCGACCTGAC38930
218GCTGGCACGAGTTTTACC38810
219GCTGTTATCCCTAGGGTA38960
220GGACATCCTAATGGTGCA38650
221GGACTTTAATCGTTGAAC36870
222GGAGCCTGTTCTAGAACC38740
223GGATGTCCTGATCCAACA38950
224GGATTAGATACCCCACTA38960
225GGATTGCGCTGTTATCCC38950
226GGCGATGTTTTTGGTAAA38900
227GGCTGGCACGAGTTTTAC38800
228GGGAAGAAATGGGCTACA38720
229GGGAGGCAAGTCGTAACA38910
230GGGGAGGCAAGTCGTAAC38900
231GGGGGTTTACGACCTCGA38940
232GGTACACTTACCATGTTA38930
233GGTCTGAACTCAGATCAC39020
234GGTCTTAGGAACCAAAAA38620
235GGTTCGTTTGTTCAACGA38770
236GTAACATGGTAAGTGTAC38930
237GTACCTTTTGCATCATGA38920
238GTCCTGATCCAACATCGA38920
239GTCTTAGGAACCAAAAAC38530
240GTGGGGTATCTAATCCCA38950
241GTTACCCTAGGGATAACA38960
242GTTTGTTCAACGATTAAA38770
243TAAAACTCGTGCCAGCCA38870
244TAACCGCGGTGGCTGGCA38950
245TAAGGGTTCGTTTGTTCA38890
246TAATCGTTGAACAAACGA38760
247TACGACCTCGATGTTGGA38920
248TAGGACTTTAATCGTTGA36890
249TAGGATGTCCTGATCCAA38970
250TCCCACTCTTTTGCCACA38660
251TCGCCTGTTTACCAAAAA38910
252TGGATCAGGACATCCTAA38940
253TGGTCTTAGGAACCAAAA38620
254TGGTGCAGCCGCTATTAA38470
255TTGGTCTTAGGAACCAAA38620