mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-11-09 09:24:41 +00:00
Eric Coissac
ad065f6853
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.
256 lines
6.5 KiB
Plaintext
256 lines
6.5 KiB
Plaintext
AAAACTCGTGCCAGCCAC 3891 0
|
|
AAACCCAAAGGACTTGGC 3890 0
|
|
AAACGAACCCTTAATAGC 3875 0
|
|
AAACTCGTGCCAGCCACC 3894 0
|
|
AAACTGGGATTAGATACC 3896 0
|
|
AAAGTCCTACGTGATCTG 3901 0
|
|
AAATCATGATGCAAAAGG 3894 0
|
|
AACAAACGAACCCTTAAT 3888 0
|
|
AACATCGAGGTCGTAAAC 3893 0
|
|
AACATGGTAAGTGTACCG 3894 0
|
|
AACCAAAAACTCTTGGTG 3854 0
|
|
AACCCAAAGGACTTGGCG 3888 0
|
|
AACCCTTAATAGCGGCTG 3858 0
|
|
AACCGCGGTGGCTGGCAC 3896 0
|
|
AACGAACCCTTAATAGCG 3860 0
|
|
AACGATTAAAGTCCTACG 3700 0
|
|
AACGTCAGGTCGAGGTGT 3894 0
|
|
AACTCAGATCACGTAGGA 3899 0
|
|
AACTCGTGCCAGCCACCG 3893 0
|
|
AACTGGGATTAGATACCC 3896 0
|
|
AAGAGTTTTTGGTTCCTA 3848 0
|
|
AAGCCTCGCCTGTTTACC 3876 0
|
|
AAGGGTTCGTTTGTTCAA 3889 0
|
|
AAGGTAGCGCAATCACTT 3889 0
|
|
AAGTCCTACGTGATCTGA 3900 0
|
|
AAGTCGTAACATGGTAAG 3893 0
|
|
AAGTGCACCTTCCGGTAC 3888 0
|
|
AAGTGTACCGGAAGGTGC 3889 0
|
|
AATAGCGGCTGCACCATT 3839 0
|
|
AATCACTTGTCTTTTAAA 3856 0
|
|
AATCATGATGCAAAAGGT 3893 0
|
|
AATCCAGGTCAGTTTCTA 3903 0
|
|
AATCGTTGAACAAACGAA 3876 0
|
|
AATGTAGCCCATTTCTTC 3871 0
|
|
ACAAACGAACCCTTAATA 3885 0
|
|
ACAAACTGGGATTAGATA 3893 0
|
|
ACAAGTGATTGCGCTACC 3889 0
|
|
ACACACCGCCCGTCACTC 3891 0
|
|
ACACCGCCCGTCACTCTC 3890 0
|
|
ACACTTACCATGTTACGA 3893 0
|
|
ACATCCTAATGGTGCAGC 3858 0
|
|
ACATCGAGGTCGTAAACC 3894 0
|
|
ACATGGTAAGTGTACCGG 3894 0
|
|
ACCAAAAACTCTTGGTGC 3875 0
|
|
ACCAAGAGTTTTTGGTTC 3857 0
|
|
ACCATGTTACGACTTGCC 3891 0
|
|
ACCATTAGGATGTCCTGA 3891 0
|
|
ACCCAAAGGACTTGGCGG 3886 0
|
|
ACCCGTCTCTGTGGCAAA 3892 0
|
|
ACCCTAGGGATAACAGCG 3895 0
|
|
ACCCTTAATAGCGGCTGC 3861 0
|
|
ACCGCCCGTCACTCTCCC 3893 0
|
|
ACCGCGGTGGCTGGCACG 3895 0
|
|
ACCGGAAGGTGCACTTGG 3887 0
|
|
ACCTCGATGTTGGATCAG 3891 0
|
|
ACCTTCCGGTACACTTAC 3893 0
|
|
ACGAACCCTTAATAGCGG 3859 0
|
|
ACGACCTCGATGTTGGAT 3889 0
|
|
ACGATTAAAGTCCTACGT 3701 0
|
|
ACGTCAGGTCGAGGTGTA 3894 0
|
|
ACGTGATCTGAGTTCAGA 3901 0
|
|
ACTCAGATCACGTAGGAC 3899 0
|
|
ACTCGTGCCAGCCACCGC 3894 0
|
|
ACTCTTTTGCCACAGAGA 3867 0
|
|
ACTGGGATTAGATACCCC 3896 0
|
|
ACTTACCATGTTACGACT 3894 0
|
|
ACTTTAATCGTTGAACAA 3876 0
|
|
AGAACAGGCTCCTCTAGG 3893 0
|
|
AGACAAGTGATTGCGCTA 3883 0
|
|
AGAGGAGCCTGTTCTAGA 3876 0
|
|
AGAGTGACGGGCGGTGTG 3890 0
|
|
AGAGTTTTTGGTTCCTAA 3851 0
|
|
AGATAGAAACTGACCTGG 3900 0
|
|
AGATCACGTAGGACTTTA 3901 0
|
|
AGCCGCTATTAAGGGTTC 3856 0
|
|
AGCCTCGCCTGTTTACCA 3889 0
|
|
AGCCTGTTCTAGAACCGA 3871 0
|
|
AGCGGCTGCACCATTAGG 3846 0
|
|
AGGAACCAAAAACTCTTG 3842 0
|
|
AGGACATCCTAATGGTGC 3866 0
|
|
AGGACTTTAATCGTTGAA 3688 0
|
|
AGGAGCCTGTTCTAGAAC 3874 0
|
|
AGGATGTCCTGATCCAAC 3897 0
|
|
AGGCAAGTCGTAACATGG 3868 0
|
|
AGGCGATGTTTTTGGTAA 3894 0
|
|
AGGGATAACAGCGCAATC 3896 0
|
|
AGGGGAGGCAAGTCGTAA 3890 0
|
|
AGGGGGTTTACGACCTCG 3894 0
|
|
AGGGTTCGTTTGTTCAAC 3888 0
|
|
AGGTAGCGCAATCACTTG 3888 0
|
|
AGTCCTACGTGATCTGAG 3900 0
|
|
AGTGGGGTATCTAATCCC 3896 0
|
|
AGTTACCCTAGGGATAAC 3895 0
|
|
AGTTTTTGGTTCCTAAGA 3848 0
|
|
ATAGAAACTGACCTGGAT 3901 0
|
|
ATAGCGGCTGCACCATTA 3837 0
|
|
ATAGTGGGGTATCTAATC 3895 0
|
|
ATCACGTAGGACTTTAAT 3880 0
|
|
ATCACTTGTCTTTTAAAT 3856 0
|
|
ATCAGGACATCCTAATGG 3892 0
|
|
ATCATGATGCAAAAGGTA 3894 0
|
|
ATCCTAATGGTGCAGCCG 3852 0
|
|
ATCGAGGTCGTAAACCCC 3894 0
|
|
ATCGGTTCTAGAACAGGC 3862 0
|
|
ATCGTTGAACAAACGAAC 3877 0
|
|
ATCTGAGTTCAGACCGGA 3902 0
|
|
ATGATGCAAAAGGTACGA 3891 0
|
|
ATGGTAAGTGTACCGGAA 3895 0
|
|
ATGGTGCAGCCGCTATTA 3840 0
|
|
ATGTAGCCCATTTCTTCC 3871 0
|
|
ATGTCCTGATCCAACATC 3892 0
|
|
ATGTTACGACTTGCCTCC 3864 0
|
|
ATGTTGGATCAGGACATC 3893 0
|
|
ATGTTTTTGGTAAACAGG 3887 0
|
|
ATTAGATACCCCACTATG 3896 0
|
|
ATTAGGATGTCCTGATCC 3893 0
|
|
ATTGCGCTGTTATCCCTA 3896 0
|
|
CAAAAACTCTTGGTGCAA 3886 0
|
|
CAAACGAACCCTTAATAG 3882 0
|
|
CAAACTGGGATTAGATAC 3895 0
|
|
CAACATCGAGGTCGTAAA 3894 0
|
|
CAACGATTAAAGTCCTAC 3691 0
|
|
CAAGTCGTAACATGGTAA 3893 0
|
|
CAAGTGCACCTTCCGGTA 3888 0
|
|
CACCATTAGGATGTCCTG 3890 0
|
|
CACCGCCCGTCACTCTCC 3888 0
|
|
CACCTTCCGGTACACTTA 3891 0
|
|
CACGTAGGACTTTAATCG 3702 0
|
|
CACTCTTTTGCCACAGAG 3856 0
|
|
CACTTACCATGTTACGAC 3894 0
|
|
CATCCTAATGGTGCAGCC 3852 0
|
|
CATCGAGGTCGTAAACCC 3894 0
|
|
CATGATGCAAAAGGTACG 3890 0
|
|
CATGGTAAGTGTACCGGA 3894 0
|
|
CATGTTACGACTTGCCTC 3866 0
|
|
CATTAGGATGTCCTGATC 3893 0
|
|
CCAAAAACTCTTGGTGCA 3883 0
|
|
CCAACATCGAGGTCGTAA 3894 0
|
|
CCAAGAGTTTTTGGTTCC 3844 0
|
|
CCACTCTTTTGCCACAGA 3879 0
|
|
CCCACTCTTTTGCCACAG 3879 0
|
|
CCCGTCTCTGTGGCAAAA 3894 0
|
|
CCCTAGGGATAACAGCGC 3898 0
|
|
CCCTTAATAGCGGCTGCA 3853 0
|
|
CCGCCCGTCACTCTCCCC 3890 0
|
|
CCGCGGTGGCTGGCACGA 3895 0
|
|
CCGGTAAAACTCGTGCCA 3847 0
|
|
CCGGTCTGAACTCAGATC 3904 0
|
|
CCGTCTCTGTGGCAAAAG 3894 0
|
|
CCTACGTGATCTGAGTTC 3899 0
|
|
CCTAGGGATAACAGCGCA 3896 0
|
|
CCTCGATGTTGGATCAGG 3892 0
|
|
CCTCGCCTGTTTACCAAA 3892 0
|
|
CCTGTTCTAGAACCGATA 3862 0
|
|
CCTTAATAGCGGCTGCAC 3850 0
|
|
CCTTCCGGTACACTTACC 3893 0
|
|
CGAACCCTTAATAGCGGC 3855 0
|
|
CGACCTCGATGTTGGATC 3890 0
|
|
CGACGGCGGTATATAGGC 3890 0
|
|
CGATGTTGGATCAGGACA 3892 0
|
|
CGATGTTTTTGGTAAACA 3886 0
|
|
CGCCTGTTTACCAAAAAC 3889 0
|
|
CGCGGTGGCTGGCACGAG 3894 0
|
|
CGCTTAGCTGTTAACTAA 3864 0
|
|
CGGTAAAACTCGTGCCAG 3856 0
|
|
CGGTCTGAACTCAGATCA 3904 0
|
|
CGGTTCTAGAACAGGCTC 3873 0
|
|
CGTAACATGGTAAGTGTA 3892 0
|
|
CGTCAGGTCGAGGTGTAG 3893 0
|
|
CGTCTCTGTGGCAAAAGA 3891 0
|
|
CGTGATCTGAGTTCAGAC 3902 0
|
|
CGTTGAACAAACGAACCC 3887 0
|
|
CGTTTGTTCAACGATTAA 3877 0
|
|
CTAAATCATGATGCAAAA 3896 0
|
|
CTAATGGTGCAGCCGCTA 3840 0
|
|
CTACGTGATCTGAGTTCA 3899 0
|
|
CTAGAACAGGCTCCTCTA 3877 0
|
|
CTAGAGGAGCCTGTTCTA 3891 0
|
|
CTAGGGATAACAGCGCAA 3897 0
|
|
CTCCGGTCTGAACTCAGA 3903 0
|
|
CTCGATGTTGGATCAGGA 3892 0
|
|
CTCGCCTGTTTACCAAAA 3892 0
|
|
CTCGTACCTTTTGCATCA 3889 0
|
|
CTCTTTTGCCACAGAGAC 3869 0
|
|
CTGAACTCAGATCACGTA 3900 0
|
|
CTGCACCATTAGGATGTC 3861 0
|
|
CTGGGATTAGATACCCCA 3895 0
|
|
CTGTTATCCCTAGGGTAA 3897 0
|
|
CTGTTTACCAAAAACATC 3886 0
|
|
CTTAATAGCGGCTGCACC 3848 0
|
|
CTTAGCTGTTAACTAAGA 3878 0
|
|
CTTAGGAACCAAAAACTC 3847 0
|
|
CTTAGTTAACAGCTAAGC 3875 0
|
|
CTTCCGGTACACTTACCA 3891 0
|
|
CTTGGATTTGCACCAAGA 3899 0
|
|
CTTTAATCGTTGAACAAA 3876 0
|
|
CTTTTGCATCATGATTTA 3896 0
|
|
GAACAAACGAACCCTTAA 3890 0
|
|
GAAGGAACTCGGCAAACA 3889 0
|
|
GACAAGTGATTGCGCTAC 3889 0
|
|
GACCTCGATGTTGGATCA 3890 0
|
|
GACTTTAATCGTTGAACA 3686 0
|
|
GAGGAGCCTGTTCTAGAA 3876 0
|
|
GAGGCGATGTTTTTGGTA 3893 0
|
|
GATAGAAACTGACCTGGA 3900 0
|
|
GATCACGTAGGACTTTAA 3900 0
|
|
GATTAAAGTCCTACGTGA 3704 0
|
|
GCAAGTCGTAACATGGTA 3891 0
|
|
GCATAGTGGGGTATCTAA 3896 0
|
|
GCCGGTAAAACTCGTGCC 3827 0
|
|
GCCTCGCCTGTTTACCAA 3890 0
|
|
GCCTGTTTACCAAAAACA 3889 0
|
|
GCGATGTTTTTGGTAAAC 3888 0
|
|
GCGCTTAGCTGTTAACTA 3899 0
|
|
GCGGCTGCACCATTAGGA 3850 0
|
|
GCTAAATCATGATGCAAA 3893 0
|
|
GCTACACCTCGACCTGAC 3893 0
|
|
GCTGGCACGAGTTTTACC 3881 0
|
|
GCTGTTATCCCTAGGGTA 3896 0
|
|
GGACATCCTAATGGTGCA 3865 0
|
|
GGACTTTAATCGTTGAAC 3687 0
|
|
GGAGCCTGTTCTAGAACC 3874 0
|
|
GGATGTCCTGATCCAACA 3895 0
|
|
GGATTAGATACCCCACTA 3896 0
|
|
GGATTGCGCTGTTATCCC 3895 0
|
|
GGCGATGTTTTTGGTAAA 3890 0
|
|
GGCTGGCACGAGTTTTAC 3880 0
|
|
GGGAAGAAATGGGCTACA 3872 0
|
|
GGGAGGCAAGTCGTAACA 3891 0
|
|
GGGGAGGCAAGTCGTAAC 3890 0
|
|
GGGGGTTTACGACCTCGA 3894 0
|
|
GGTACACTTACCATGTTA 3893 0
|
|
GGTCTGAACTCAGATCAC 3902 0
|
|
GGTCTTAGGAACCAAAAA 3862 0
|
|
GGTTCGTTTGTTCAACGA 3877 0
|
|
GTAACATGGTAAGTGTAC 3893 0
|
|
GTACCTTTTGCATCATGA 3892 0
|
|
GTCCTGATCCAACATCGA 3892 0
|
|
GTCTTAGGAACCAAAAAC 3853 0
|
|
GTGGGGTATCTAATCCCA 3895 0
|
|
GTTACCCTAGGGATAACA 3896 0
|
|
GTTTGTTCAACGATTAAA 3877 0
|
|
TAAAACTCGTGCCAGCCA 3887 0
|
|
TAACCGCGGTGGCTGGCA 3895 0
|
|
TAAGGGTTCGTTTGTTCA 3889 0
|
|
TAATCGTTGAACAAACGA 3876 0
|
|
TACGACCTCGATGTTGGA 3892 0
|
|
TAGGACTTTAATCGTTGA 3689 0
|
|
TAGGATGTCCTGATCCAA 3897 0
|
|
TCCCACTCTTTTGCCACA 3866 0
|
|
TCGCCTGTTTACCAAAAA 3891 0
|
|
TGGATCAGGACATCCTAA 3894 0
|
|
TGGTCTTAGGAACCAAAA 3862 0
|
|
TGGTGCAGCCGCTATTAA 3847 0
|
|
TTGGTCTTAGGAACCAAA 3862 0
|