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refine can now expose mafft requirements and functests updated for pysam 0.22
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145 changes: 0 additions & 145 deletions
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repo_utils/test_files/external/fake_mafft/lookup/fm_34fd267f3c76809107dec2452a21e62a.msa
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repo_utils/test_files/external/fake_mafft/lookup/fm_3af60a231e26aa93504606f040b84a53.msa
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| >syndip_1_chr20:20320239-20320620 | ||
| ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag | ||
| taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat | ||
| atatgtaatatatattatatatatgtaatatatataatatatgtaatatatgtaatatat | ||
| attatatatgtaatataatatatgtaatatatattatatatgtaatatata--------- | ||
| ---------------------------atatatgtaatatatattatatatgtaatataa | ||
| tatatgtaatatatattatatatgtaatatatattacatatattatatatgcaatatata | ||
| ttatatatattatatatgcaatatatattatatatattatatatgcaatatatattatat | ||
| atgcaatatatattatatatattatatatgcaatatatattatatatattacatatgtaa | ||
| tatatattacatatgtaatatataatatattatatattacatatgtaatatataatatat | ||
| tatatattacatatgtaatatataatatatattacatatgtaatatataatatatattac | ||
| atatgtaatatattatatattacatatgtaatatattatatattacatatgtaatatatt | ||
| atatattacatatgtaatatattatatattacatatgtaatatattatatattacatatg | ||
| taatatatataatatattacatatgtaatatataatatattatatatgtaatatatatta | ||
| catatataatatatataatatatatgtaatatattatatatattatatatgtaatatata | ||
| ttacatatataatatatattatatatattacatatattatatatgtaatatatattacat | ||
| atgtaatatatgtaatatatattacatatgtaatatatattatatatgtaatatatatta | ||
| catatattatatatgtaatatatattatatatattatatatgtaatgtataatatatata | ||
| ttatatatgtaatatatattatatataatatatgtaatatatattatatatgtaatgtat | ||
| attatatatattatatatgtaatgtatattatatataatatatgtaatgtatattatata | ||
| tgtaatatatattatgtatattatatatgtaatatatattatatatattatatatgtaat | ||
| atatattatatatattatatatgtaatatatattatatatattatatatgtaatatatat | ||
| tatatatattatatatgtaatatatattatatatattatatatgtaatatatattatata | ||
| tattatatatgtaatatatattatatatattatatatgtaatatatattatatatattat | ||
| atatgtaatatatattatatatattatatatgtaatatatattatatatattatatatgt | ||
| aatatatattatatatattatatatgtaatatatattatatatattatatatgtaatata | ||
| tattatatatattatatatgtaatatatattatatatattatatatgtaatatatatata | ||
| tttaaaaacagaaccattatcttttagagatacatactgaagtgtctggagacatgcttc | ||
| aagataacccag | ||
| >syndip_2_chr20:20320239-20320620 | ||
| ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag | ||
| taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat | ||
| atatgtaatatatattatatatatgtaatatatataatatatgtaatatatgtaatatat | ||
| attatatatgtaatataatatatgtaatatatattatatatgtaatatata--------- | ||
| ---------------------------atatatgtaat----------------atataa | ||
| tatatgtaatatatattatatatgtaatatata--atatatattatatatgtaatatata | ||
| tatatttaaaaacagaaccattatcttttagagatac----------------------- | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ---------------------------------atactgaagtgtctggagacatgcttc | ||
| aagataacccag | ||
| >p:HG002_1_chr20:20320239-20320620 | ||
| ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag | ||
| taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat | ||
| atatgtaatatatattatatatatgtaatatatataatatatgtaatatatgtaatatat | ||
| attatatatgtaatataatatatgtaatatatattatatatgtaatatata--------- | ||
| ---------------------------atatatgtaat----------------atataa | ||
| tatatgtaatatatattatatatgtaatatata--atatatattatatatgtaatatata | ||
| tatatttaaaaacagaaccattatcttttagagatac----------------------- | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ---------------------------------atactgaagtgtctggagacatgcttc | ||
| aagataacccag | ||
| >p:HG002_2_chr20:20320239-20320620 | ||
| ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag | ||
| taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat | ||
| atatgtaatatatattatatatatgtaatatatataatatatgtaatatatgtaatatat | ||
| attatatatgtaatataatatatgtaatatatattatatatgtaatatataatatatgta | ||
| atatatatattatatatgtaatatataatatatgtaatatatattatatatgtaatataa | ||
| tatatgtaatatatattatatatgtaatatatattacatatattatatatgcaatatata | ||
| ttatatatattatatatgcaatatatattatatatattatatatgcaatatatattatat | ||
| atgcaatatatattatatatattatatatgcaatatatattatatatattacatatgtaa | ||
| tatatattacatatgtaatatataatatattatatattacatatgtaatatataatatat | ||
| tatatattacatatgtaatatataatatatattacatatgtaatatataatatatattac | ||
| atatgtaatatattatatattacatatgtaatatattatatattacatatgtaatatatt | ||
| atatattacatatgtaatatattatatattacatatgtaatatattatatattacatatg | ||
| taatatatataatatattacatatgtaatatataatatattatatatgtaatatatatta | ||
| catatataatatatataatatatatgtaatatattatatatattatatatgtaatatata | ||
| ttacatatataatatatattatatatattacatatattatatatgtaatatatattacat | ||
| atgtaatatatgtaatatatattacatatgtaatatatattatatatgtaatatatatta | ||
| catatattatatatgtaatatatattatatatattatatatgtaatgtataatatatata | ||
| ttatatatgtaatatatattatatataatatatgtaatatatattatatatgtaatgtat | ||
| attatatatattatatatgtaatgtatattatatataatatatgtaatgtatattatata | ||
| tgtaatatatattatgtatattatatatgtaatatatattatatatattatatatgtaat | ||
| atatattatatatattatatatgtaatatatattatatatattatatatgtaatatatat | ||
| tatatatattatatatgtaatatatattatatatattatatatgtaatatatattatata | ||
| tattatatatgtaatatatattatatatattatatatgtaatatatattatatatattat | ||
| atatgtaatatatattatatatattatatatgtaatatatattatatatattatatatgt | ||
| aatatatattatatatattatatatgtaatatatattatatatattatatatgtaatata | ||
| tatgtaatatatattatatatgtaatatataatatatattatatatgtaatatatatata | ||
| tttaaaaacagaaccattatcttttagagatacatactgaagtgtctggagacatgcttc | ||
| aagataacccag | ||
| >ref_chr20:20320239-20320620 | ||
| ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag | ||
| taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat | ||
| atatgtaatatatattatatatatgtaatatatataatatatgtaatatatgtaatatat | ||
| attatatatgtaatataatatatgtaatatatattatatatgtaatatata--------- | ||
| ---------------------------atatatgtaat----------------atataa | ||
| tatatgtaatatatattatatatgtaatatata--atatatattatatatgtaatatata | ||
| tatatttaaaaacagaaccattatcttttagagatac----------------------- | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ---------------------------------atactgaagtgtctggagacatgcttc | ||
| aagataacccag |
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