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Collapse genotype collapsing preserves phasing bar Very minor speed improvement for collapse
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145
repo_utils/test_files/external/fake_mafft/lookup/fm_34fd267f3c76809107dec2452a21e62a.msa
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,145 @@ | ||
| >syndip_1_chr20:20320239-20320620 | ||
| ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag | ||
| taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat | ||
| atatgtaatatatattatatatatgtaatatatataatatatgtaatatattatatatat | ||
| gtaatatatataatatatgtaatatatattatatatgtaatatatataatatatgtaata | ||
| tatattatatatgtaatata----atatatgtaatatatattatatatgtaatatataat | ||
| atatgtaatatatattatatatgtaatataatatatgtaatatatattatatatgtaata | ||
| tatattacatatattatatatgcaatatatattatatatattatatatgcaatatatatt | ||
| atatatattatatatgcaatatatattatatatgcaatatatattatatatattatatat | ||
| gcaatatatattatatatattacatatgtaatatatattacatatgtaatatataatata | ||
| ttatatattacatatgtaatatataatatattatatattacatatgtaatatataatata | ||
| tattacatatgtaatatataatatatattacatatgtaatatattatatattacatatgt | ||
| aatatattatatattacatatgtaatatattatatattacatatgtaatatattatatat | ||
| tacatatgtaatatattatatattacatatgtaatatatataatatattacatatgtaat | ||
| atataatatattatatatgtaatatatattacatatataatatatataatatatatgtaa | ||
| tatattatatatattatatatgtaatatatattacatatataatatatattatatatatt | ||
| acatatattatatatgtaatatatattacatatgtaatatatgtaatatatattacatat | ||
| gtaatatatattatatatgtaatatatattacatatattatatatgtaatatatattata | ||
| tatattatatatgtaatgtataatatatatattatatatgtaatatatattatatataat | ||
| atatgtaatatatattatatatgtaatgtatattatatatattatatatgtaatgtatat | ||
| tatatataatatatgtaatgtatattatatatgtaatatatattatgtatattatatatg | ||
| taatatatattatatatattatatatgtaatatatattatatatattatatatgtaatat | ||
| atattatatatattatatatgtaatatatattatatatattatatatgtaatatatatta | ||
| tatatattatatatgtaatatatattatatatattatatatgtaatatatattatatata | ||
| ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat | ||
| atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa | ||
| tatatattatatatattatatatgtaatatatattatatatattatatatgtaatatata | ||
| ttatatatattatatatgtaatatatatatatttaaaaacagaaccattatcttttagag | ||
| atacatactgaagtgtctggagacatgcttcaagataacccag | ||
| >syndip_2_chr20:20320239-20320620 | ||
| ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag | ||
| taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat | ||
| atatgtaatatata---------------------------ttatatatatgtaatatat | ||
| ataatatatgtaatatatgtaatatatattatatatgta----atataatatatgtaata | ||
| tatattatatatgtaatatata--------------------atatatgtaatatataat | ||
| atatgtaatatatattatatatgtaatata-------taatatatattatatatgtaata | ||
| tatatatatttaaaaacagaaccattatcttttagagatac------------------- | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ----atactgaagtgtctggagacatgcttcaagataacccag | ||
| >p:HG002_1_chr20:20320239-20320620 | ||
| ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag | ||
| taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat | ||
| atatgtaatatata---------------------------ttatatatatgtaatatat | ||
| ataatatatgtaatatatgtaatatatattatatatgta----atataatatatgtaata | ||
| tatattatatatgtaatatata--------------------atatatgtaatatataat | ||
| atatgtaatatatattatatatgtaatata-------taatatatattatatatgtaata | ||
| tatatatatttaaaaacagaaccattatcttttagagatac------------------- | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ----atactgaagtgtctggagacatgcttcaagataacccag | ||
| >p:HG002_2_chr20:20320239-20320620 | ||
| ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag | ||
| taaagatggtatttcagatatatagatatatatatat--tatatatgtaatatatataat | ||
| atatgtaatatgta--atatatataatatatgtaatatatattatatatatgtaatatat | ||
| ataatatatgtaatatatgtaatatatattatatatgta----atataatatatgtaata | ||
| tatattatatatgtaatatataatatatgtaatatatatattatatatgtaatatataat | ||
| atatgtaatatatattatatatgtaatataatatatgtaatatatattatatatgtaata | ||
| tatattacatatattatatatgcaatatatattatatatattatatatgcaatatatatt | ||
| atatatattatatatgcaatatatattatatatgcaatatatattatatatattatatat | ||
| gcaatatatattatatatattacatatgtaatatatattacatatgtaatatataatata | ||
| ttatatattacatatgtaatatataatatattatatattacatatgtaatatataatata | ||
| tattacatatgtaatatataatatatattacatatgtaatatattatatattacatatgt | ||
| aatatattatatattacatatgtaatatattatatattacatatgtaatatattatatat | ||
| tacatatgtaatatattatatattacatatgtaatatatataatatattacatatgtaat | ||
| atataatatattatatatgtaatatatattacatatataatatatataatatatatgtaa | ||
| tatattatatatattatatatgtaatatatattacatatataatatatattatatatatt | ||
| acatatattatatatgtaatatatattacatatgtaatatatgtaatatatattacatat | ||
| gtaatatatattatatatgtaatatatattacatatattatatatgtaatatatattata | ||
| tatattatatatgtaatgtataatatatatattatatatgtaatatatattatatataat | ||
| atatgtaatatatattatatatgtaatgtatattatatatattatatatgtaatgtatat | ||
| tatatataatatatgtaatgtatattatatatgtaatatatattatgtatattatatatg | ||
| taatatatattatatatattatatatgtaatatatattatatatattatatatgtaatat | ||
| atattatatatattatatatgtaatatatattatatatattatatatgtaatatatatta | ||
| tatatattatatatgtaatatatattatatatattatatatgtaatatatattatatata | ||
| ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat | ||
| atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa | ||
| tatatattatatatattatatatgtaatatatatgtaatatatattatatatgtaatata | ||
| taatatatattatatatgtaatatatatatatttaaaaacagaaccattatcttttagag | ||
| atacatactgaagtgtctggagacatgcttcaagataacccag | ||
| >ref_chr20:20320239-20320620 | ||
| ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag | ||
| taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat | ||
| atatgtaatatata---------------------------ttatatatatgtaatatat | ||
| ataatatatgtaatatatgtaatatatattatatatgta----atataatatatgtaata | ||
| tatattatatatgtaatatata--------------------atatatgtaatatataat | ||
| atatgtaatatatattatatatgtaatata-------taatatatattatatatgtaata | ||
| tatatatatttaaaaacagaaccattatcttttagagatac------------------- | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ----atactgaagtgtctggagacatgcttcaagataacccag |
130 changes: 130 additions & 0 deletions
130
repo_utils/test_files/external/fake_mafft/lookup/fm_a3b02bde8a503aab8bb0da7f33f98a9d.msa
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,130 @@ | ||
| >syndip_1_chr20:63028776-63029503 | ||
| caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg | ||
| agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca | ||
| aacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg | ||
| cctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctccg | ||
| cgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc | ||
| cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc | ||
| tccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccggg | ||
| cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg | ||
| ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccc | ||
| cgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcc | ||
| cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggt | ||
| cccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcag | ||
| gtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgc | ||
| aggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgt | ||
| gcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgt | ||
| gtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctcc | ||
| gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct | ||
| ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc | ||
| ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc | ||
| gcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc | ||
| gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct | ||
| ccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg | ||
| ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt | ||
| catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca | ||
| t | ||
| >syndip_2_chr20:63028776-63029503 | ||
| caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg | ||
| agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca | ||
| aa---------------------------------------------------------- | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| -------------------------------------------------------cgcac | ||
| ccga-------------------------------------------------------- | ||
| ------------------------------------------------------------ | ||
| --------gtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct | ||
| ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc | ||
| ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc | ||
| gcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctcc | ||
| gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct | ||
| ccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagtttg | ||
| ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt | ||
| catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca | ||
| t | ||
| >p:HG002_1_chr20:63028776-63029503 | ||
| caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg | ||
| agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca | ||
| aa---------------------------------------------------------- | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| -------------------------------------------------------cgcac | ||
| ccga-------------------------------------------------------- | ||
| ------------------------------------------------------------ | ||
| --------gtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct | ||
| ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc | ||
| ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc | ||
| gcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctcc | ||
| gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct | ||
| ccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagtttg | ||
| ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt | ||
| catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca | ||
| t | ||
| >p:HG002_2_chr20:63028776-63029503 | ||
| caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg | ||
| agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca | ||
| aacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg | ||
| cctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctccg | ||
| cgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc | ||
| cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc | ||
| tccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccggg | ||
| cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg | ||
| ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccc | ||
| cgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcc | ||
| cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggt | ||
| cccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcag | ||
| gtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgc | ||
| aggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgt | ||
| gcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgt | ||
| gtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctcc | ||
| gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct | ||
| ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc | ||
| ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc | ||
| gcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc | ||
| gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct | ||
| ccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg | ||
| ccaacgtccatgcacgtctcagcctctcagcctggactggacaactcggcttcgggaatt | ||
| catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgaattca | ||
| t | ||
| >ref_chr20:63028776-63029503 | ||
| caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg | ||
| agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca | ||
| aa---------------------------------------------------------- | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| -------------------------------------------------------cgcac | ||
| ccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgt | ||
| gtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctcc | ||
| gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct | ||
| ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc | ||
| ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc | ||
| gcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctcc | ||
| gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct | ||
| ccgcgtctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg | ||
| ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt | ||
| catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca | ||
| t |
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