PyPI - partis-bcr - Versions diffs - 1.0.11.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl - Mend

partis-bcr 1.0.11.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (652) hide show

test/paired/new-results/test/simu/igk.yaml ADDED Viewed

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+ {"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igk", "functionalities": {}, "seqs": {"v": {"IGKV1-12*01": "GACATCCAGATGACCCAGTCTCCATCTTCCGTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGCTGGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTCC", "IGKV1-27*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCGAGTCAGGGCATTAGCAATTATTTAGCCTGGTATCAGCAGAAACCAGGGAAAGTTCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAATCAGGGGTCCCATCTCGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATGTTGCAACTTATTACTGTCAAAAGTATAACAGTGCCCCTCC", "IGKV1-33*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCC", "IGKV1-5*01": "GACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGAGTATTAGTAGCTGGTTGGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACTTATTACTGCCAACAGTATAATAGTTATTCTCC", "IGKV1-8*03": "GCCATCCGGATGACCCAGTCTCCATCCTCACTCTCTGCATCTACAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCTGCCTGCAGTCTGAAGATTTTGCAACTTATTACTGTCAACAGTATTATAGTTACCCTCC", "IGKV1-9*01": "GACATCCAGTTGACCCAGTCTCCATCCTTCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGGGCATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGCTTAATAGTTACCCTCC", "IGKV1D-13*02": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCA", "IGKV1D-39*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCC", "IGKV2-24*01": "GATATTGTGATGACCCAGACTCCACTCTCCTCACCTGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTACACAGTGATGGAAACACCTACTTGAGTTGGCTTCAGCAGAGGCCAGGCCAGCCTCCAAGACTCCTAATTTATAAGATTTCTAACCGGTTCTCTGGGGTCCCAGACAGATTCAGTGGCAGTGGGGCAGGGACAGATTTCACACTGAAAATCAGCAGGGTGGAAGCTGAGGATGTCGGGGTTTATTACTGCATGCAAGCTACACAATTTCCTCA", "IGKV2-30*01": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCTCC", "IGKV2D-28*01": "GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCTCC", "IGKV3-11*01": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCC", "IGKV3-15*01": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCC", "IGKV3-20*01": "GAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCTCC", "IGKV4-1*02": "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCCTCC", "IGKV6-21*01": "GAAATTGTGCTGACTCAGTCTCCAGACTTTCAGTCTGTGACTCCAAAGGAGAAAGTCACCATCACCTGCCGGGCCAGTCAGAGCATTGGTAGTAGCTTACACTGGTACCAGCAGAAACCAGATCAGTCTCCAAAGCTCCTCATCAAGTATGCTTCCCAGTCCTTCTCAGGGGTCCCCTCGAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACCCTCACCATCAATAGCCTGGAAGCTGAAGATGCTGCAACGTATTACTGTCATCAGAGTAGTAGTTTACCTCA"}, "d": {"IGKDx-x*x": "A"}, "j": {"IGKJ1*01": "GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "IGKJ2*01": "TGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*03": "TGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*04": "TGTGCAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ3*01": "ATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "IGKJ4*01": "GCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "IGKJ5*01": "GATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"}}, "cyst-positions": {"IGKV1-5*01": 261, "IGKV1-9*01": 261, "IGKV3-20*01": 264, "IGKV2-24*01": 276, "IGKV1-33*01": 261, "IGKV1-12*01": 261, "IGKV2D-28*01": 276, "IGKV1-27*01": 261, "IGKV6-21*01": 261, "IGKV3-11*01": 261, "IGKV1D-39*01": 261, "IGKV1D-13*02": 261, "IGKV3-15*01": 261, "IGKV4-1*02": 279, "IGKV2-30*01": 276, "IGKV1-8*03": 261}, "phen-positions": {"IGKJ3*01": 7, "IGKJ5*01": 7, "IGKJ4*01": 7, "IGKJ2*04": 8, "IGKJ2*03": 8, "IGKJ2*01": 8, "IGKJ1*01": 7}}, "partitions": [{"logprob": 0.0, "n_clusters": 7, "n_procs": 1, "partition": [["6728f9fb1f-igk", "84b9b0a5db-igk", "25beda54e8-igk", "a385b6b9c0-igk", "762f4ed65b-igk", "293677779b-igk", "539dc7162b-igk", "7fc27267b4-igk", "c074eb0544-igk", "5414307e18-igk", "1dc717a47d-igk", "fa79e38212-igk"], ["3590a73b2b-igk", "486333046a-igk"], ["5b83db58bc-igk", "70cc01a590-igk", "8c82b5df7c-igk"], ["dde37df0f3-igk", "4e698cd55b-igk"], ["a32678cdd4-igk"], ["4879a2a0d7-igk", "7777388536-igk", "69e29aff11-igk", "c449e7d496-igk", "b8dd0bbe5b-igk", "831950bd07-igk", "1df0b0d259-igk", "2bbe5f9b28-igk", "9f7c316b7a-igk"], ["2b1422c0aa-igk", "5cb34a1703-igk", "053a8abb6c-igk", "39fc72ec75-igk", "d3edbb8447-igk", "031d868683-igk", "1b28490bf6-igk"]]}], "events": [{"qr_gap_seqs": ["GAAATAGTGATGACGCAGTCTCCAGTCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCA.......AGCAGCAACTTAACCTGGTACCAGCAGAAACCTGGCCAGGCCCCCAGGCTCCTCATCTATGGTGCATCCACCAGAGCCACTGGTATCCCAGCCACAGGTTCAGTGGCAGTGGCTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTGTTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "", "", "", "", "", "", "", "", "", "GAAATAGTGATGACGCAGTCTCCAGC....CTGTCTGTGTCTCCACGGGAAAGAGTCACCCTCTCCTGCAGAGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAATCTGGCCAGGCTCCCAGGCTCCTCATCTTTGGTGCATCCACCAGAGCCACTGGTTGTGGTAATATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTGTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGTAGTTTATTACTGTTAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGAAGTTTTAGTCGCAGTCTCCAGCCACCCTGTCTGTGTCTACAGGGGGAAGAGCCACCCTCTCCTCCAGGGTCAGTCAGAGTATTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTG....................................GTGCCAGTGGATCTGGGACAGAGTTCACTCTCACCATTAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAGC"], "gl_gap_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGC..CAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "", "", "", "", "", "", "", "", "", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGG.........TATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGA.........CGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "indel_reversed_seqs": ["GAAATAGTGATGACGCAGTCTCCAGTCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAACCTGGTACCAGCAGAAACCTGGCCAGGCCCCCAGGCTCCTCATCTATGGTGCATCCACCAGAGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGCTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTGTTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "", "", "", "", "", "", "", "", "", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCACGGGAAAGAGTCACCCTCTCCTGCAGAGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAATCTGGCCAGGCTCCCAGGCTCCTCATCTTTGGTGCATCCACCAGAGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTGTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGTAGTTTATTACTGTTAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTACAGGGGGAAGAGCCACCCTCTCCTCCAGGGTCAGTCAGAGTATTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGAGCCACTGGTATCCCAGCCAGGTTCAGTGCCAGTGGATCTGGGACAGAGTTCACTCTCACCATTAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAGC"], "reco_id": "8a9d39afe0", "tree": "[&R] ((((5414307e18-igk:0.008502932147128023,1dc717a47d-igk:0.008502932147128023)ajt:0.008122880405858672,(((c074eb0544-igk:0.014991685301204651,(fa79e38212-igk:0.014055471951124665,(84b9b0a5db-igk:0.013541867892427785,293677779b-igk:0.013541867892427785)oux:0.00051360406210676)hxy:0.0009362133446551766)ijo:0.000864750165343496,25beda54e8-igk:0.015856435462673284)lot:0.00011011364305165203,(6728f9fb1f-igk:0.015715928326901298,((539dc7162b-igk:0.0037746814180675773,7fc27267b4-igk:0.0037746814180675773)dmy:0.009194508628349793,762f4ed65b-igk:0.012969190047967318)jmo:0.0027467382742841456)flx:0.000250620783163485)lmr:0.0006592634473392585)gvw:0.000310518390578505,a385b6b9c0-igk:0.016936330943797692)jwy:0.0018146457098906887)bkq:0.0;", "unique_ids": ["6728f9fb1f-igk", "84b9b0a5db-igk", "25beda54e8-igk", "a385b6b9c0-igk", "762f4ed65b-igk", "293677779b-igk", "539dc7162b-igk", "7fc27267b4-igk", "c074eb0544-igk", "5414307e18-igk", "1dc717a47d-igk", "fa79e38212-igk"], "invalid": false, "v_gene": "IGKV3-15*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 30, "mut_freqs": [0.018808777429467086, 0.03761755485893417, 0.03134796238244514, 0.018808777429467086, 0.01567398119122257, 0.02821316614420063, 0.018808777429467086, 0.012539184952978056, 0.034482758620689655, 0.02821316614420063, 0.02821316614420063, 0.03134796238244514], "n_mutations": [6, 12, 10, 6, 5, 9, 6, 4, 11, 9, 9, 10], "input_seqs": ["GAAATAGTGATGACGCAGTCTCCAGTCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAAGCAGCAACTTAACCTGGTACCAGCAGAAACCTGGCCAGGCCCCCAGGCTCCTCATCTATGGTGCATCCACCAGAGCCACTGGTATCCCAGCCACAGGTTCAGTGGCAGTGGCTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTGTTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCACTCTGTCTGTGTCTCCAGGGGGAAGGGCCACCCTCTCCTGCAGGGCCAGTCAGAGTATTAGCAGCAACTTAGCCTGGTACCAGCAGAAACATGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGAGCCACTAGTATCCCAACCAAGTTCAGTGCCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTTTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAGC", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAAGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACGAGCAGAAACCTCGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAAAGCCACTGGTATCCCAGCCAGGTTCAGTGCCAGTGGGTCTGGGACAGAGTTCACTCTCACGACCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCACCAGTATAATAACTGGTGGACGTTCGGCCAAGGGGCCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGACCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTATCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCTTCCACCAGAGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCCCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTAGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCTGCCACCCTGTCTCTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGAGCCACTGGTATCCCATCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGAGGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGGAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTATTAGCAGCAACTTAGCCTGTTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCTTCCACCAGAGCCACTGGTATCCCAGCCAGGTTCAGTGCCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGCTTATTACTGTCAGCAGTATAATAACTGGTGGACATTCGGCCAAGGGACCAAGGTGGAAATCAAGC", "GAAATAGTGATGACGCTGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCGGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGTCTCCTCATCTATGGTGGATCCACCAGAGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTACTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCGGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGTCTCCTCATCTATGGTGCATCCACCAGAGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTACTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCAGCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGAAGGGCCAGTCAAAGTATTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGAGCCACTGGTACCCCAGCCAGGTTCAGTGCGAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAATTTATTACTGTCAGCGGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAGC", "GAAATAGTGATGACGCAGTCTCCACCCACCCTGTCTGTGTCTCCACGGGAAAGAGCCACCCTCTCCTGCAGGGCTAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATATTTGGTGCATCCACCAGAGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCGCTGTCACCATCAGCAGCCTGCAGTCTGAAGATTTTCCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCTGTCTGTGTCTCCACGGGAAAGAGTCACCCTCTCCTGCAGAGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAATCTGGCCAGGCTCCCAGGCTCCTCATCTTTGGTGCATCCACCAGAGCCACTGGTTGTGGTAATATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTGTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGTAGTTTATTACTGTTAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGAAGTTTTAGTCGCAGTCTCCAGCCACCCTGTCTGTGTCTACAGGGGGAAGAGCCACCCTCTCCTCCAGGGTCAGTCAGAGTATTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGGTGCCAGTGGATCTGGGACAGAGTTCACTCTCACCATTAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAGC"], "has_shm_indels": [true, false, false, false, false, false, false, false, false, false, true, true], "naive_seq": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[], [], [], [], [], [], [], [], [], [], [], []], "v_3p_del": 6, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false, false], "in_frames": [false, true, true, true, true, true, true, true, true, true, false, true], "stops": [true, false, false, true, false, false, false, false, true, false, true, true], "paired-uids": [["6728f9fb1f-igh"], [], ["25beda54e8-igh", "5d404a8547-igh", "5d404a8547-igl"], ["a385b6b9c0-igh"], [], ["293677779b-igh"], ["11f41b5f10-igh", "539dc7162b-igh"], ["45de550151-igl", "7fc27267b4-igh"], ["6d2eb72d4b-igh", "c074eb0544-igh"], ["5414307e18-igh"], ["1dc717a47d-igh"], ["fa79e38212-igh"]], "loci": ["igk", "igk", "igk", "igk", "igk", "igk", "igk", "igk", "igk", "igk", "igk", "igk"], "codon_positions": {"v": 261, "j": 288}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "reco_id": "ca482b4daf", "tree": "[&R] (((1bb77dbdd8-igk:-0.0,486333046a-igk:-0.0)jux:0.0,3590a73b2b-igk:-0.0)egh:-0.0)hmv:0.0;", "unique_ids": ["3590a73b2b-igk", "486333046a-igk"], "invalid": false, "v_gene": "IGKV3-11*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 36, "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCCGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCCGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC"], "naive_seq": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCCGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[], []], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "paired-uids": [["3590a73b2b-igh"], ["486333046a-igh"]], "loci": ["igk", "igk"], "codon_positions": {"v": 261, "j": 294}}, {"qr_gap_seqs": ["", "", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCAGCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "gl_gap_seqs": ["", "", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCC..CAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "indel_reversed_seqs": ["", "", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "reco_id": "8ff5ec4520", "tree": "[&R] ((70cc01a590-igk:-0.0,(5b83db58bc-igk:-0.0,8c82b5df7c-igk:-0.0)euv:0.0)doz:-0.0)alx:0.0;", "unique_ids": ["5b83db58bc-igk", "70cc01a590-igk", "8c82b5df7c-igk"], "invalid": false, "v_gene": "IGKV3-15*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 30, "mut_freqs": [0.0, 0.0, 0.0], "n_mutations": [0, 0, 0], "input_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCAGCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "has_shm_indels": [false, false, true], "naive_seq": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[], [], []], "v_3p_del": 6, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, false], "stops": [false, false, false], "paired-uids": [["504e3941e6-igh", "504e3941e6-igl", "5b83db58bc-igh"], ["fa02aeb02e-igh"], ["8c82b5df7c-igh"]], "loci": ["igk", "igk", "igk"], "codon_positions": {"v": 261, "j": 288}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "reco_id": "6564755f20", "tree": "[&R] ((4e698cd55b-igk:0.001172468977992632,dde37df0f3-igk:0.001172468977992632)dku:0.0014777104579907138)mrx:0.0;", "unique_ids": ["dde37df0f3-igk", "4e698cd55b-igk"], "invalid": false, "v_gene": "IGKV1-12*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ3*01", "cdr3_length": 33, "mut_freqs": [0.0, 0.003105590062111801], "n_mutations": [0, 1], "input_seqs": ["GACATCCAGATGACCCAGTCTCCATCTTCCGTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGCTGGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "GACATCCAGATGACCCAGTCTCCATCTTCCGTGTCTGCATCTGTAGGAGACAGAGTCACGATCACTTGTCGGGCGAGTCAGGGTATTAGCAGCTGGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC"], "has_shm_indels": [false, false], "naive_seq": "GACATCCAGATGACCCAGTCTCCATCTTCCGTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGCTGGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "duplicates": [[], []], "v_3p_del": 2, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "paired-uids": [["dde37df0f3-igh"], ["4e698cd55b-igh"]], "loci": ["igk", "igk"], "codon_positions": {"v": 261, "j": 291}}, {"has_shm_indels": [true], "qr_gap_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAA..................GGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGAC....TTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "gl_gap_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "indel_reversed_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "reco_id": "b2144fab8e", "tree": "[&R] ((a32678cdd4-igk:-0.0,6daaa9b771-igk:-0.0)ads:-0.0)aeh:0.0;", "unique_ids": ["a32678cdd4-igk"], "invalid": false, "v_gene": "IGKV3-15*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 30, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "naive_seq": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[]], "v_3p_del": 6, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [false], "paired-uids": [["a32678cdd4-igh", "fd0c4f0f17-igh", "fd0c4f0f17-igl"]], "loci": ["igk"], "codon_positions": {"v": 261, "j": 288}}, {"qr_gap_seqs": ["GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAA..AGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "", "", "", "", "", "", ""], "gl_gap_seqs": ["GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "", "", "", "", "", "", ""], "indel_reversed_seqs": ["GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "", "", "", "", "", "", ""], "reco_id": "182e588062", "tree": "[&R] ((((c449e7d496-igk:-0.0,2bbe5f9b28-igk:-0.0)doz:-0.0,((1df0b0d259-igk:-0.0,4879a2a0d7-igk:-0.0)kow:-0.0,b8dd0bbe5b-igk:-0.0)juy:-0.0)lpx:-0.0,(7777388536-igk:-0.0,((69e29aff11-igk:-0.0,831950bd07-igk:-0.0)cqx:-0.0,9f7c316b7a-igk:-0.0)jsy:-0.0)kuz:-0.0)aej:-0.0)bwx:0.0;", "unique_ids": ["4879a2a0d7-igk", "7777388536-igk", "69e29aff11-igk", "c449e7d496-igk", "b8dd0bbe5b-igk", "831950bd07-igk", "1df0b0d259-igk", "2bbe5f9b28-igk", "9f7c316b7a-igk"], "invalid": false, "v_gene": "IGKV4-1*02", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 33, "mut_freqs": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "n_mutations": [0, 0, 0, 0, 0, 0, 0, 0, 0], "input_seqs": ["GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAAAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC"], "has_shm_indels": [true, false, false, false, false, false, false, false, false], "naive_seq": "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[], [], [], [], [], [], [], [], []], "v_3p_del": 4, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false], "in_frames": [false, true, true, true, true, true, true, true, true], "stops": [true, false, false, false, false, false, false, false, false], "paired-uids": [["4879a2a0d7-igh"], ["7777388536-igh"], ["1bd9242383-igl", "69e29aff11-igh"], ["c449e7d496-igh"], ["b8dd0bbe5b-igh"], ["831950bd07-igh"], ["1df0b0d259-igh"], ["2bbe5f9b28-igh"], ["9f7c316b7a-igh"]], "loci": ["igk", "igk", "igk", "igk", "igk", "igk", "igk", "igk", "igk"], "codon_positions": {"v": 279, "j": 309}}, {"has_shm_indels": [false, false, false, false, true, true, false], "qr_gap_seqs": ["", "", "", "", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCT...TCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGTCCCTAACGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCGCTTGGGACAGATTTCACTCTCACCATCACCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAG...ACCAAGCTGGAGATCAAAC", ""], "gl_gap_seqs": ["", "", "", "", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAA.GCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATC...TGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", ""], "indel_reversed_seqs": ["", "", "", "", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGTCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCACCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", ""], "reco_id": "d217d13f25", "tree": "[&R] ((053a8abb6c-igk:0.002579919728288003,(((5cb34a1703-igk:0.00022332081592492988,f5dedfcd67-igk:0.00022332081592492988)uvy:0.0007244571733808729,(2b1422c0aa-igk:0.0005927327741661682,39fc72ec75-igk:0.0005927327741661682)lqu:0.00035504521513963453)efv:0.0013234461181477395,((1b28490bf6-igk:0.0018482221322063217,d3edbb8447-igk:0.0018482221322063217)hlv:2.8527657173184614e-05,031d868683-igk:0.0018767497892095062)gpw:0.0003944743181440362)gly:0.00030869562073446047)pqv:7.025970777784327e-05)cuy:0.0;", "unique_ids": ["2b1422c0aa-igk", "5cb34a1703-igk", "053a8abb6c-igk", "39fc72ec75-igk", "d3edbb8447-igk", "031d868683-igk", "1b28490bf6-igk"], "invalid": false, "v_gene": "IGKV1D-39*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ2*03", "cdr3_length": 36, "mut_freqs": [0.003076923076923077, 0.003076923076923077, 0.006153846153846154, 0.003076923076923077, 0.006153846153846154, 0.006153846153846154, 0.003076923076923077], "n_mutations": [1, 1, 2, 1, 2, 2, 1], "input_seqs": ["GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAACCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTTCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGTCCCTAACGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCGCTTGGGACAGATTTCACTCTCACCATCACCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGACCAAGCTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC"], "naive_seq": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCCGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "duplicates": [[], [], [], [], [], [], []], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, false, true, true], "stops": [false, false, false, false, true, false, false], "paired-uids": [[], ["5cb34a1703-igh"], ["053a8abb6c-igh"], [], ["19e0f0b170-igh", "19e0f0b170-igl", "d3edbb8447-igh"], ["031d868683-igh"], ["1b28490bf6-igh"]], "loci": ["igk", "igk", "igk", "igk", "igk", "igk", "igk"], "codon_positions": {"v": 261, "j": 294}}]}

test/paired/new-results/test/simu/igl.yaml ADDED Viewed

@@ -0,0 +1 @@

+ {"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV1-51*02": "CAGTCTGTGTTGACGCAGCCGCCCTCAGTGTCTGCGGCCCCAGGACAGAAGGTCACCATCTCCTGCTCTGGAAGCAGCTCCAACATTGGGAATAATTATGTATCCTGGTACCAGCAGCTCCCAGGAACAGCCCCCAAACTCCTCATCTATGAAAATAATAAGCGACCCTCAGGGATTCCTGACCGATTCTCTGGCTCCAAGTCTGGCACGTCAGCCACCCTGGGCATCACCGGACTCCAGACTGGGGACGAGGCCGATTATTACTGCGGAACATGGGATAGCAGCCTGAGTGCTGG", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC", "IGLV3-1*01": "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGCA", "IGLV3-19*01": "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATCT", "IGLV3-27*01": "TCCTATGAGCTGACACAGCCATCCTCAGTGTCAGTGTCTCCGGGACAGACAGCCAGGATCACCTGCTCAGGAGATGTACTGGCAAAAAAATATGCTCGGTGGTTCCAGCAGAAGCCAGGCCAGGCCCCTGTGCTGGTGATTTATAAAGACAGTGAGCGGCCCTCAGGGATCCCTGAGCGATTCTCCGGCTCCAGCTCAGGGACCACAGTCACCTTGACCATCAGCGGGGCCCAGGTTGAGGATGAGGCTGACTATTACTGTTACTCTGCGGCTGACAACAATCT", "IGLV4-60*03": "CAGCCTGTGCTGACTCAATCATCCTCTGCCTCTGCTTCCCTGGGATCCTCGGTCAAGCTCACCTGCACTCTGAGCAGTGGGCACAGTAGCTACATCATCGCATGGCATCAGCAGCAGCCAGGGAAGGCCCCTCGGTACTTGATGAAGCTTGAAGGTAGTGGAAGCTACAACAAGGGGAGCGGAGTTCCTGATCGCTTCTCAGGCTCCAGCTCTGGGGCTGACCGCTACCTCACCATCTCCAACCTCCAGTCTGAGGATGAGGCTGATTATTACTGTGAGACCTGGGACAGTAACACTCA", "IGLV7-46*04": "CAGGCTGTGGTGACTCAGGAGCCCTCACTGACTGTGTCCCCAGGAGGGACAGTCACTCTCACCTGTGGCTCCAGCACTGGAGCTGTCACCAGTGGTCATTATCCCTACTGGTTCCAGCAGAAGCCTGGCCAAGCCCCCAGGACACTGATTTATGATACAAGCAACAAACACTCCTGGACCCCTGCCCGGTTCTCAGGCTCCCTCCTTGGGGGCAAAGCTGCCCTGACCCTTTCGGGTGCGCAGCCTGAGGATGAGGCTGAGTATTACTGCTTGCTCTCCTATAGTGGTGCTCGG", "IGLV8-61*01": "CAGACTGTGGTGACCCAGGAGCCATCGTTCTCAGTGTCCCCTGGAGGGACAGTCACACTCACTTGTGGCTTGAGCTCTGGCTCAGTCTCTACTAGTTACTACCCCAGCTGGTACCAGCAGACCCCAGGCCAGGCTCCACGCACGCTCATCTACAGCACAAACACTCGCTCTTCTGGGGTCCCTGATCGCTTCTCTGGCTCCATCCTTGGGAACAAAGCTGCCCTCACCATCACGGGGGCCCAGGCAGATGATGAATCTGATTATTACTGTGTGCTGTATATGGGTAGTGGCATTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ2*01": "TGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"}}, "cyst-positions": {"IGLV8-61*01": 267, "IGLV2-14*04": 267, "IGLV4-60*03": 273, "IGLV2-23*02": 267, "IGLV1-40*01": 267, "IGLV3-1*01": 258, "IGLV1-51*02": 264, "IGLV7-46*04": 267, "IGLV3-27*01": 258, "IGLV3-19*01": 258}, "phen-positions": {"IGLJ1*01": 7, "IGLJ2*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": 0.0, "n_clusters": 3, "n_procs": 1, "partition": [["b68b8d0fe2-igl", "de762b8ce4-igl", "552c9f1e08-igl", "c8a03324cc-igl", "d068457847-igl", "0bfaf8b4b1-igl", "8c03b80be0-igl", "f4ebbe68a7-igl", "d8138c32a6-igl", "922ea4413e-igl", "a55e058517-igl", "383777b7c5-igl"], ["898ab41392-igl", "5d404a8547-igl", "fd0c4f0f17-igl"], ["a9c9c3afba-igl", "1bd9242383-igl", "45de550151-igl", "652adbce26-igl", "504e3941e6-igl", "19e0f0b170-igl"]]}], "events": [{"has_shm_indels": [false, false, false, false, false, false, false, false, false, true, false, false], "qr_gap_seqs": ["", "", "", "", "", "", "", "", "", "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGATAGTCAGGATCACATGCCAAGAAGAGAGCCTCAGAAGCTATTATGCAAGCTCGTACCAGCAGAAGCCAGGACAGGCCCCTATCCTTGTCATCTATAGTAAGAACAACCGGCCCTCAGGGATCCCAGACCGATTCTTTGGCTCC........AAACACAGCTTCCTTGACAATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTGCTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "", ""], "gl_gap_seqs": ["", "", "", "", "", "", "", "", "", "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "", ""], "indel_reversed_seqs": ["", "", "", "", "", "", "", "", "", "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGATAGTCAGGATCACATGCCAAGAAGAGAGCCTCAGAAGCTATTATGCAAGCTCGTACCAGCAGAAGCCAGGACAGGCCCCTATCCTTGTCATCTATAGTAAGAACAACCGGCCCTCAGGGATCCCAGACCGATTCTTTGGCTCCAGCTCAGAAAACACAGCTTCCTTGACAATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTGCTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "", ""], "reco_id": "e707c96016", "tree": "[&R] (((((3a41497d91-igl:0.007385162951159356,d068457847-igl:0.007385162951159356)bkm:0.005605303670959556,45eb339259-igl:0.0129904666254787)iqr:0.002648926846099352,(552c9f1e08-igl:0.01466725887272979,de762b8ce4-igl:0.01466725887272979)gis:0.0009721345962724225)ahz:0.004634256160450372,((c8a03324cc-igl:0.0025550433855388802,922ea4413e-igl:0.0025550433855388802)mos:0.016905476324571775,((8c03b80be0-igl:0.011287736113761764,((f4ebbe68a7-igl:0.0015841087168501067,383777b7c5-igl:0.0015841087168501067)fnr:0.0002666556744881951,((0bfaf8b4b1-igl:0.0014312958996758355,a55e058517-igl:0.0014312958996758355)hkt:0.0003340799418143904,d8138c32a6-igl:0.001765375841378233)beo:8.538855010565957e-05)adh:0.009436971722983427)efn:0.00737350252108383,b68b8d0fe2-igl:0.01866123863932531)clt:0.0007992810697774085)ags:0.0008131299216937824)buv:0.009406482169521176)alp:0.0;", "unique_ids": ["b68b8d0fe2-igl", "de762b8ce4-igl", "552c9f1e08-igl", "c8a03324cc-igl", "d068457847-igl", "0bfaf8b4b1-igl", "8c03b80be0-igl", "f4ebbe68a7-igl", "d8138c32a6-igl", "922ea4413e-igl", "a55e058517-igl", "383777b7c5-igl"], "invalid": false, "v_gene": "IGLV3-19*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ2*01", "cdr3_length": 39, "mut_freqs": [0.04, 0.021538461538461538, 0.04, 0.04, 0.03076923076923077, 0.021538461538461538, 0.03076923076923077, 0.018461538461538463, 0.021538461538461538, 0.036923076923076927, 0.018461538461538463, 0.018461538461538463], "n_mutations": [13, 7, 13, 13, 10, 7, 10, 6, 7, 12, 6, 6], "input_seqs": ["TCTTCTGAGCTGACTCAGGACCCTGCTCTGTCTGTGGCCTTGGGACAGATAGTCAGGATCACATGCCAAAAAGACAGCCTCAGAAGCTATTATGCAAGCTGGTTCCAGCAGAAGCCAGGACAGGCTCCTGTACTTGTCATCTATGGTAAAAGCAACCGGCCCTCAGTGATCCCAGACCGATTATTTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGCGGCTCAGGCGAAACATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGATAGTCAGGATCACATGCTAAGAAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCGTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCAATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTCTTACTGTAACTCCCGGGACAGCAGTGGTAACGATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCTTCTGAGCTGACTCAGGACCCTGCTGCGTCTGTGGCCTTGGGACAGATAGTCAGGATCGCATGCCAAGAAGACAGCCTCAGAAGCTATTATCCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTCGGGCTCAGGCAGAAGATGAGGCTGCCTCTTACTGTAACTCCCGGGACAACAGTGATAACGATGTGGTATTCGTCGGAGGGACCAAGCTGACCGTCCTAG", "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGATAGTCGGGATCACATGCCAAGAAGAGAGCCTCAGAAGCTATTATGCAAGCTCGTACCAGCAGAAGCCAGGACAGGCCCCTATCCTTGTCATCTATAGTAAGAACAACCGGCCCTCAGGGATCCCAGACCGATTCTTTGGCTCCAGCTCAGAAAACACAGCTTCCTTGACAATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTGCTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCTTCTGAGCTGACTCAGGACCATGCTGTGTCTGTGGCCTTGGGACAGATAGTCAGGATCACATGCCAAGAAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGAAAGGCCCCTGTACTTGTCATCTATGGTAAAAACTATCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTAACCATCACTGGGGCTGAGGCGGAAGATGAGGCTGACTCTTACTGTAACTCCCGGGACAGCAGTGGTAACGATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGATAGTCAGGATCACATGCCAAGAAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCGTCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTATTTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACCATTACTGTAACTCCCGGGACAACAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCTTCTGAGCTTACTCAGGACCCTGCTGTGTCTGTGGCCTTAGGACAGATAGTCAGGATCACATGCCAAGAAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAATCGGCCCTCAGGGATCCCAGACCGATTATTTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGCTAAGCATCTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGATAGTCAGGATCACATGCCAAGAAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCGTCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTATTTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACCATTACTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGATAGTCAGGATCACATGCCAAGAAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCGTCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTATTTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACCATTACTGTAACTTCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGATAGTCAGGATCACATGCCAAGAAGAGAGCCTCAGAAGCTATTATGCAAGCTCGTACCAGCAGAAGCCAGGACAGGCCCCTATCCTTGTCATCTATAGTAAGAACAACCGGCCCTCAGGGATCCCAGACCGATTCTTTGGCTCCAAACACAGCTTCCTTGACAATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTGCTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGATAGTCAGGATCACATGCCAAGAAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCGTCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTATTTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACCATTACTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGATAGTCAGGATCACATGCCAAGAAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCGTCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTATTTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACCATTACTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "naive_seq": "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[], [], [], [], [], [], [], [], [], [], [], []], "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true, false, true, true], "stops": [false, true, false, false, false, false, false, false, false, true, false, false], "paired-uids": [["b68b8d0fe2-igh"], ["de762b8ce4-igh", "ebb52c305d-igh"], ["552c9f1e08-igh"], ["898ab41392-igh", "898ab41392-igl", "c8a03324cc-igh"], ["d068457847-igh"], ["0bfaf8b4b1-igh"], ["8c03b80be0-igh"], ["f4ebbe68a7-igh"], ["652adbce26-igh", "652adbce26-igl"], ["922ea4413e-igh"], ["a55e058517-igh"], ["383777b7c5-igh"]], "loci": ["igl", "igl", "igl", "igl", "igl", "igl", "igl", "igl", "igl", "igl", "igl", "igl"], "codon_positions": {"v": 258, "j": 294}}, {"qr_gap_seqs": ["", "CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", ""], "gl_gap_seqs": ["", "CAGTCTGCCCTG...ACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", ""], "indel_reversed_seqs": ["", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", ""], "reco_id": "dd76478982", "tree": "[&R] (((fd0c4f0f17-igl:-0.0,5d404a8547-igl:-0.0)bqw:-0.0,898ab41392-igl:-0.0)fpy:-0.0)cgn:0.0;", "unique_ids": ["898ab41392-igl", "5d404a8547-igl", "fd0c4f0f17-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0, 0.0, 0.0], "n_mutations": [0, 0, 0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false, true, false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[], [], []], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "paired-uids": [["898ab41392-igh", "c8a03324cc-igh", "c8a03324cc-igl"], ["25beda54e8-igh", "25beda54e8-igk", "5d404a8547-igh"], ["a32678cdd4-igh", "a32678cdd4-igk", "fd0c4f0f17-igh"]], "loci": ["igl", "igl", "igl"], "codon_positions": {"v": 267, "j": 303}}, {"has_shm_indels": [false, false, true, false, false, false], "qr_gap_seqs": ["", "", "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGC.GGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGG.....CCAAGCTGACCGTCCTAG", "", "", ""], "gl_gap_seqs": ["", "", "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "", "", ""], "indel_reversed_seqs": ["", "", "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "", "", ""], "reco_id": "da8c9d16ae", "tree": "[&R] (((((fa02aeb02e-igl:-0.0,a9c9c3afba-igl:-0.0)efs:-0.0,(((652adbce26-igl:-0.0,45de550151-igl:-0.0)giy:-0.0,1bd9242383-igl:-0.0)axy:-0.0,(11f41b5f10-igl:-0.0,6d2eb72d4b-igl:-0.0)cfj:-0.0)hns:-0.0)hjv:-0.0,(19e0f0b170-igl:-0.0,504e3941e6-igl:-0.0)emn:-0.0)iwz:-0.0,ebb52c305d-igl:-0.0)eju:-0.0)bgr:0.0;", "unique_ids": ["a9c9c3afba-igl", "1bd9242383-igl", "45de550151-igl", "652adbce26-igl", "504e3941e6-igl", "19e0f0b170-igl"], "invalid": false, "v_gene": "IGLV3-1*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ2*01", "cdr3_length": 33, "mut_freqs": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "n_mutations": [0, 0, 0, 0, 0, 0], "input_seqs": ["TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGGCCAAGCTGACCGTCCTAG", "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "naive_seq": "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[], [], [], [], [], []], "v_3p_del": 2, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false], "in_frames": [true, true, false, true, true, true], "stops": [false, false, true, false, false, false], "paired-uids": [[], ["69e29aff11-igh", "69e29aff11-igk"], ["7fc27267b4-igh", "7fc27267b4-igk"], ["652adbce26-igh", "d8138c32a6-igl"], ["504e3941e6-igh", "5b83db58bc-igh", "5b83db58bc-igk"], ["19e0f0b170-igh", "d3edbb8447-igh", "d3edbb8447-igk"]], "loci": ["igl", "igl", "igl", "igl", "igl", "igl"], "codon_positions": {"v": 258, "j": 288}}]}

test/paired/new-results/test/simu/meta.yaml ADDED Viewed

@@ -0,0 +1 @@

+ {"6728f9fb1f-igh": {"locus": "igh", "paired-uids": ["6728f9fb1f-igk"]}, "25beda54e8-igh": {"locus": "igh", "paired-uids": ["25beda54e8-igk", "5d404a8547-igh", "5d404a8547-igl"]}, "a385b6b9c0-igh": {"locus": "igh", "paired-uids": ["a385b6b9c0-igk"]}, "293677779b-igh": {"locus": "igh", "paired-uids": ["293677779b-igk"]}, "539dc7162b-igh": {"locus": "igh", "paired-uids": ["11f41b5f10-igh", "539dc7162b-igk"]}, "7fc27267b4-igh": {"locus": "igh", "paired-uids": ["45de550151-igl", "7fc27267b4-igk"]}, "c074eb0544-igh": {"locus": "igh", "paired-uids": ["6d2eb72d4b-igh", "c074eb0544-igk"]}, "5414307e18-igh": {"locus": "igh", "paired-uids": ["5414307e18-igk"]}, "1dc717a47d-igh": {"locus": "igh", "paired-uids": ["1dc717a47d-igk"]}, "fa79e38212-igh": {"locus": "igh", "paired-uids": ["fa79e38212-igk"]}, "3590a73b2b-igh": {"locus": "igh", "paired-uids": ["3590a73b2b-igk"]}, "486333046a-igh": {"locus": "igh", "paired-uids": ["486333046a-igk"]}, "1bb77dbdd8-igh": {"locus": "igh", "paired-uids": []}, "5b83db58bc-igh": {"locus": "igh", "paired-uids": ["504e3941e6-igh", "504e3941e6-igl", "5b83db58bc-igk"]}, "8c82b5df7c-igh": {"locus": "igh", "paired-uids": ["8c82b5df7c-igk"]}, "dde37df0f3-igh": {"locus": "igh", "paired-uids": ["dde37df0f3-igk"]}, "4e698cd55b-igh": {"locus": "igh", "paired-uids": ["4e698cd55b-igk"]}, "6daaa9b771-igh": {"locus": "igh", "paired-uids": ["3a41497d91-igh"]}, "a32678cdd4-igh": {"locus": "igh", "paired-uids": ["a32678cdd4-igk", "fd0c4f0f17-igh", "fd0c4f0f17-igl"]}, "4879a2a0d7-igh": {"locus": "igh", "paired-uids": ["4879a2a0d7-igk"]}, "7777388536-igh": {"locus": "igh", "paired-uids": ["7777388536-igk"]}, "69e29aff11-igh": {"locus": "igh", "paired-uids": ["1bd9242383-igl", "69e29aff11-igk"]}, "c449e7d496-igh": {"locus": "igh", "paired-uids": ["c449e7d496-igk"]}, "b8dd0bbe5b-igh": {"locus": "igh", "paired-uids": ["b8dd0bbe5b-igk"]}, "831950bd07-igh": {"locus": "igh", "paired-uids": ["831950bd07-igk"]}, "1df0b0d259-igh": {"locus": "igh", "paired-uids": ["1df0b0d259-igk"]}, "2bbe5f9b28-igh": {"locus": "igh", "paired-uids": ["2bbe5f9b28-igk"]}, "9f7c316b7a-igh": {"locus": "igh", "paired-uids": ["9f7c316b7a-igk"]}, "f5dedfcd67-igh": {"locus": "igh", "paired-uids": []}, "5cb34a1703-igh": {"locus": "igh", "paired-uids": ["5cb34a1703-igk"]}, "053a8abb6c-igh": {"locus": "igh", "paired-uids": ["053a8abb6c-igk"]}, "d3edbb8447-igh": {"locus": "igh", "paired-uids": ["19e0f0b170-igh", "19e0f0b170-igl", "d3edbb8447-igk"]}, "031d868683-igh": {"locus": "igh", "paired-uids": ["031d868683-igk"]}, "1b28490bf6-igh": {"locus": "igh", "paired-uids": ["1b28490bf6-igk"]}, "b68b8d0fe2-igh": {"locus": "igh", "paired-uids": ["b68b8d0fe2-igl"]}, "de762b8ce4-igh": {"locus": "igh", "paired-uids": ["de762b8ce4-igl", "ebb52c305d-igh"]}, "552c9f1e08-igh": {"locus": "igh", "paired-uids": ["552c9f1e08-igl"]}, "c8a03324cc-igh": {"locus": "igh", "paired-uids": ["898ab41392-igh", "898ab41392-igl", "c8a03324cc-igl"]}, "d068457847-igh": {"locus": "igh", "paired-uids": ["d068457847-igl"]}, "0bfaf8b4b1-igh": {"locus": "igh", "paired-uids": ["0bfaf8b4b1-igl"]}, "8c03b80be0-igh": {"locus": "igh", "paired-uids": ["8c03b80be0-igl"]}, "f4ebbe68a7-igh": {"locus": "igh", "paired-uids": ["f4ebbe68a7-igl"]}, "922ea4413e-igh": {"locus": "igh", "paired-uids": ["922ea4413e-igl"]}, "a55e058517-igh": {"locus": "igh", "paired-uids": ["a55e058517-igl"]}, "383777b7c5-igh": {"locus": "igh", "paired-uids": ["383777b7c5-igl"]}, "3a41497d91-igh": {"locus": "igh", "paired-uids": ["6daaa9b771-igh"]}, "898ab41392-igh": {"locus": "igh", "paired-uids": ["898ab41392-igl", "c8a03324cc-igh", "c8a03324cc-igl"]}, "5d404a8547-igh": {"locus": "igh", "paired-uids": ["25beda54e8-igh", "25beda54e8-igk", "5d404a8547-igl"]}, "fd0c4f0f17-igh": {"locus": "igh", "paired-uids": ["a32678cdd4-igh", "a32678cdd4-igk", "fd0c4f0f17-igl"]}, "ebb52c305d-igh": {"locus": "igh", "paired-uids": ["de762b8ce4-igh", "de762b8ce4-igl"]}, "652adbce26-igh": {"locus": "igh", "paired-uids": ["652adbce26-igl", "d8138c32a6-igl"]}, "6d2eb72d4b-igh": {"locus": "igh", "paired-uids": ["c074eb0544-igh", "c074eb0544-igk"]}, "11f41b5f10-igh": {"locus": "igh", "paired-uids": ["539dc7162b-igh", "539dc7162b-igk"]}, "504e3941e6-igh": {"locus": "igh", "paired-uids": ["504e3941e6-igl", "5b83db58bc-igh", "5b83db58bc-igk"]}, "19e0f0b170-igh": {"locus": "igh", "paired-uids": ["19e0f0b170-igl", "d3edbb8447-igh", "d3edbb8447-igk"]}, "fa02aeb02e-igh": {"locus": "igh", "paired-uids": ["70cc01a590-igk"]}, "6728f9fb1f-igk": {"locus": "igk", "paired-uids": ["6728f9fb1f-igh"]}, "84b9b0a5db-igk": {"locus": "igk", "paired-uids": []}, "25beda54e8-igk": {"locus": "igk", "paired-uids": ["25beda54e8-igh", "5d404a8547-igh", "5d404a8547-igl"]}, "a385b6b9c0-igk": {"locus": "igk", "paired-uids": ["a385b6b9c0-igh"]}, "762f4ed65b-igk": {"locus": "igk", "paired-uids": []}, "293677779b-igk": {"locus": "igk", "paired-uids": ["293677779b-igh"]}, "539dc7162b-igk": {"locus": "igk", "paired-uids": ["11f41b5f10-igh", "539dc7162b-igh"]}, "7fc27267b4-igk": {"locus": "igk", "paired-uids": ["45de550151-igl", "7fc27267b4-igh"]}, "c074eb0544-igk": {"locus": "igk", "paired-uids": ["6d2eb72d4b-igh", "c074eb0544-igh"]}, "5414307e18-igk": {"locus": "igk", "paired-uids": ["5414307e18-igh"]}, "1dc717a47d-igk": {"locus": "igk", "paired-uids": ["1dc717a47d-igh"]}, "fa79e38212-igk": {"locus": "igk", "paired-uids": ["fa79e38212-igh"]}, "3590a73b2b-igk": {"locus": "igk", "paired-uids": ["3590a73b2b-igh"]}, "486333046a-igk": {"locus": "igk", "paired-uids": ["486333046a-igh"]}, "5b83db58bc-igk": {"locus": "igk", "paired-uids": ["504e3941e6-igh", "504e3941e6-igl", "5b83db58bc-igh"]}, "70cc01a590-igk": {"locus": "igk", "paired-uids": ["fa02aeb02e-igh"]}, "8c82b5df7c-igk": {"locus": "igk", "paired-uids": ["8c82b5df7c-igh"]}, "dde37df0f3-igk": {"locus": "igk", "paired-uids": ["dde37df0f3-igh"]}, "4e698cd55b-igk": {"locus": "igk", "paired-uids": ["4e698cd55b-igh"]}, "a32678cdd4-igk": {"locus": "igk", "paired-uids": ["a32678cdd4-igh", "fd0c4f0f17-igh", "fd0c4f0f17-igl"]}, "4879a2a0d7-igk": {"locus": "igk", "paired-uids": ["4879a2a0d7-igh"]}, "7777388536-igk": {"locus": "igk", "paired-uids": ["7777388536-igh"]}, "69e29aff11-igk": {"locus": "igk", "paired-uids": ["1bd9242383-igl", "69e29aff11-igh"]}, "c449e7d496-igk": {"locus": "igk", "paired-uids": ["c449e7d496-igh"]}, "b8dd0bbe5b-igk": {"locus": "igk", "paired-uids": ["b8dd0bbe5b-igh"]}, "831950bd07-igk": {"locus": "igk", "paired-uids": ["831950bd07-igh"]}, "1df0b0d259-igk": {"locus": "igk", "paired-uids": ["1df0b0d259-igh"]}, "2bbe5f9b28-igk": {"locus": "igk", "paired-uids": ["2bbe5f9b28-igh"]}, "9f7c316b7a-igk": {"locus": "igk", "paired-uids": ["9f7c316b7a-igh"]}, "2b1422c0aa-igk": {"locus": "igk", "paired-uids": []}, "5cb34a1703-igk": {"locus": "igk", "paired-uids": ["5cb34a1703-igh"]}, "053a8abb6c-igk": {"locus": "igk", "paired-uids": ["053a8abb6c-igh"]}, "39fc72ec75-igk": {"locus": "igk", "paired-uids": []}, "d3edbb8447-igk": {"locus": "igk", "paired-uids": ["19e0f0b170-igh", "19e0f0b170-igl", "d3edbb8447-igh"]}, "031d868683-igk": {"locus": "igk", "paired-uids": ["031d868683-igh"]}, "1b28490bf6-igk": {"locus": "igk", "paired-uids": ["1b28490bf6-igh"]}, "b68b8d0fe2-igl": {"locus": "igl", "paired-uids": ["b68b8d0fe2-igh"]}, "de762b8ce4-igl": {"locus": "igl", "paired-uids": ["de762b8ce4-igh", "ebb52c305d-igh"]}, "552c9f1e08-igl": {"locus": "igl", "paired-uids": ["552c9f1e08-igh"]}, "c8a03324cc-igl": {"locus": "igl", "paired-uids": ["898ab41392-igh", "898ab41392-igl", "c8a03324cc-igh"]}, "d068457847-igl": {"locus": "igl", "paired-uids": ["d068457847-igh"]}, "0bfaf8b4b1-igl": {"locus": "igl", "paired-uids": ["0bfaf8b4b1-igh"]}, "8c03b80be0-igl": {"locus": "igl", "paired-uids": ["8c03b80be0-igh"]}, "f4ebbe68a7-igl": {"locus": "igl", "paired-uids": ["f4ebbe68a7-igh"]}, "d8138c32a6-igl": {"locus": "igl", "paired-uids": ["652adbce26-igh", "652adbce26-igl"]}, "922ea4413e-igl": {"locus": "igl", "paired-uids": ["922ea4413e-igh"]}, "a55e058517-igl": {"locus": "igl", "paired-uids": ["a55e058517-igh"]}, "383777b7c5-igl": {"locus": "igl", "paired-uids": ["383777b7c5-igh"]}, "898ab41392-igl": {"locus": "igl", "paired-uids": ["898ab41392-igh", "c8a03324cc-igh", "c8a03324cc-igl"]}, "5d404a8547-igl": {"locus": "igl", "paired-uids": ["25beda54e8-igh", "25beda54e8-igk", "5d404a8547-igh"]}, "fd0c4f0f17-igl": {"locus": "igl", "paired-uids": ["a32678cdd4-igh", "a32678cdd4-igk", "fd0c4f0f17-igh"]}, "a9c9c3afba-igl": {"locus": "igl", "paired-uids": []}, "1bd9242383-igl": {"locus": "igl", "paired-uids": ["69e29aff11-igh", "69e29aff11-igk"]}, "45de550151-igl": {"locus": "igl", "paired-uids": ["7fc27267b4-igh", "7fc27267b4-igk"]}, "652adbce26-igl": {"locus": "igl", "paired-uids": ["652adbce26-igh", "d8138c32a6-igl"]}, "504e3941e6-igl": {"locus": "igl", "paired-uids": ["504e3941e6-igh", "5b83db58bc-igh", "5b83db58bc-igk"]}, "19e0f0b170-igl": {"locus": "igl", "paired-uids": ["19e0f0b170-igh", "d3edbb8447-igh", "d3edbb8447-igk"]}}

test/paired/new-results/test.log CHANGED Viewed

@@ -33,7 +33,7 @@ hmm
       hmm step time: 2.1
   writing hmms     removed 3  genes from glfo (leaving v 6  d 15  j 4)
 (0.3 sec)
-      total time: 4.0
+      total time: 3.9
 [44mcache-parameters[0m [94migk[0m:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 [91mrun[0m partis cache-parameters --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -68,7 +68,7 @@ hmm
          infra time: 0.9
       hmm step time: 1.4
   writing hmms     removed 0  genes from glfo (leaving v 5  d 1  j 5)
-(0.3 sec)
+(0.4 sec)
       total time: 2.8
 [44mcache-parameters[0m [94migl[0m:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -91,7 +91,7 @@ smith-waterman  (writing parameters)
       kept 14 (0.667) unproductive
         writing sw results to test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml
     writing parameters to test/paired/new-results/test/parameters/simu/igl/sw (0.3 sec)
-    water time: 0.4  (ig-sw 0.3  processing 0.0)
+    water time: 0.4  (ig-sw 0.4  processing 0.0)
   writing hmms     removed 7  genes from glfo (leaving v 3  d 1  j 2)
 (0.1 sec)
 hmm
@@ -103,8 +103,8 @@ hmm
       hmm step time: 0.9
   writing hmms     removed 0  genes from glfo (leaving v 3  d 1  j 2)
 (0.1 sec)
-      total time: 1.6
-      total time: 12.2
+      total time: 1.7
+      total time: 12.3
 [92mpartition-new-simu[0m               partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu
   [93mwarning[0m ignoring --plot-annotation-performance for paired clustering since it's going to be a bit fiddly to implement
 [44mpartition[0m [94migh[0m:
@@ -124,7 +124,7 @@ smith-waterman
 hmm
   caching all 56 naive sequences (1.0s)
     collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
-  50 clusters with 10 procs (0.6s)
+  50 clusters with 10 procs (0.5s)
    44 clusters with 7 procs (0.5s)
    36 clusters with 5 procs (0.4s)
    31 clusters with 3 procs (0.3s)
@@ -137,8 +137,8 @@ getting annotations for final partition
     [93mwarning[0m skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: db63559ea9-igh
 (0.0 sec)
-    subcluster annotation time 1.0
-      total time: 5.0
+    subcluster annotation time 0.9
+      total time: 4.9
 [44mpartition[0m [94migk[0m:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 [91mrun[0m partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igk --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/ref-results/test/simu/igk.yaml --outfname test/paired/new-results/partition-new-simu/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -260,7 +260,7 @@ smith-waterman
 hmm
   subcluster annotating 15 clusters with steps:  (0.3s) (0.1s)
     subcluster annotation time 0.4
-      total time: 0.4
+      total time: 0.5
 [94migh+igl[0m: synchronizing heavy and light chain cluster paths
     removing badly + unpaired seqs:  kept 7 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): [94mh[0m 3  [92ml[0m 4
             note: discarding unpaired seqs in families with no (well-)paired seqs (i.e. families that are all either unpaired or paired to the other/wrong light chain), rather than keeping track of them to re-add later
@@ -331,7 +331,7 @@ hmm
         [94mh[0m   20 --> 23   [91m+3[0m
         [95mk[0m    6 --> 15   [91m+9[0m
         [92ml[0m    3 --> 8    [91m+5[0m
-      total time: 20.0
+      total time: 19.9
 [92msubset-partition-new-simu[0m        partis subset-partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --n-subsets 2 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu
   note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
   --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -362,7 +362,7 @@ hmm
     merging parameters from 2 subdirs (e.g. test/paired/new-results/subset-partition-new-simu/isub-0) to test/paired/new-results/subset-partition-new-simu/merged-subsets
 [91mrun[0m partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu --input-metafnames test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/merged-subsets --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile
         log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
-      total time: 68.1
+      total time: 68.6
 [92mseed-partition-new-simu[0m          partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --max-ccf-fail-frac 0.10 --is-simu --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk --seed-loci igh:igk --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/seed-partition-new-simu
    removing seqs very different from seed seq
                            wrong/no     removed      singly         kept   missing
@@ -400,7 +400,7 @@ getting annotations for final partition
     reading output
         read 12 hmm output lines with 17 sequences in 12 events  (0 failures)
       hmm step time: 0.3
-      total time: 2.0
+      total time: 1.9
 [44mpartition[0m [94migk[0m:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 [91mrun[0m partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/input-seqs-igk.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -552,7 +552,7 @@ hmm
    N clusters with all seqs:
         [94mh[0m   12 --> 1    [91m-11[0m
         [95mk[0m    2 --> 1    [91m-1[0m
-      total time: 9.4
+      total time: 9.3
 [92mget-selection-metrics-new-simu[0m   partis get-selection-metrics --dont-write-git-info --paired-loci --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
 [44mget-selection-metrics[0m [94migh+igk[0m:[94m igh[0m
 [91mrun[0m partis get-selection-metrics --locus igh --dont-write-git-info --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv --refuse-to-cache-parameters --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml
@@ -676,7 +676,7 @@ hmm
       total time: 5.6
 [92mcache-parameters-data[0m            partis cache-parameters --dont-write-git-info --paired-loci --infname test/paired-data/all-seqs.fa --parameter-dir test/paired/new-results/test/parameters/data --n-max-queries 100 --random-seed 1 --n-procs 10
   note: --paired-outdir is not set, so there will be no persistent record of the results (except the parameter directory).
-[91mrun[0m extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/749815/meta.yaml --n-max-queries 100
+[91mrun[0m extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/888813/meta.yaml --n-max-queries 100
   --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
   extract_pairing_info(): read 100 sequences with 48 droplet ids
     droplet id separators (set automatically): _  indices: [0]
@@ -687,9 +687,9 @@ hmm
         2           42     0.875
         3            2     0.042
         4            2     0.042
-[91mrun[0m split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/749815 --input-metafname /tmp/runner/hmms/749815/meta.yaml --n-max-queries 100
+[91mrun[0m split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/888813 --input-metafname /tmp/runner/hmms/888813/meta.yaml --n-max-queries 100
   --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
-  --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
+  --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/888813/meta.yaml: paired-uids
     read pairing info for 100 seqs from input meta file
   running vsearch on 100 sequences:
     igh:   49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
@@ -712,10 +712,10 @@ totals: igh 48 igk 37 igl 15
                2   0.13   [94mh[0m [92ml[0m
                1   0.07   [94mh[0m [95mk[0m
                1   0.07   [94mh[0m [94mh[0m [95mk[0m
-writing to /tmp/runner/hmms/749815/
-  igh: 48 to 749815/igh.fa
-  igk: 37 to 749815/igk.fa
-  igl: 15 to 749815/igl.fa
+writing to /tmp/runner/hmms/888813/
+  igh: 48 to 888813/igh.fa
+  igk: 37 to 888813/igk.fa
+  igl: 15 to 888813/igl.fa
 writing to paired subdirs
     igh+igk:
       igh: 36 / 48 to igh+igk/igh.fa
@@ -724,8 +724,8 @@ writing to paired subdirs
       igh: 15 / 48 to igh+igl/igh.fa
       igl: 15 / 15 to igh+igl/igl.fa
 [44mcache-parameters[0m [94migh[0m:
-[91mrun[0m partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/749815/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/749815/meta.yaml
-  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
+[91mrun[0m partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/888813/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/888813/meta.yaml
+  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/888813/meta.yaml: paired-uids
 caching parameters
   vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.0 sec
     keeping 23 / 198 v genes
@@ -744,7 +744,7 @@ smith-waterman  (writing parameters)
     writing parameters to test/paired/new-results/test/parameters/data/igh/sw (2.0 sec)
     water time: 2.2  (ig-sw 2.1  processing 0.1)
   writing hmms     removed 13 genes from glfo (leaving v 23  d 19  j 6)
-(0.9 sec)
+(1.0 sec)
 hmm
     reading output
         read 48 hmm output lines with 48 sequences in 48 events  (0 failures)
@@ -752,11 +752,11 @@ hmm
          infra time: 2.0
       hmm step time: 3.0
   writing hmms     removed 1  genes from glfo (leaving v 23  d 18  j 6)
-(0.9 sec)
+(1.0 sec)
       total time: 7.5
 [44mcache-parameters[0m [94migk[0m:
-[91mrun[0m partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/749815/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/749815/meta.yaml
-  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
+[91mrun[0m partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/888813/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/888813/meta.yaml
+  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/888813/meta.yaml: paired-uids
 caching parameters
   vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.0 sec
     keeping 16 / 64 v genes
@@ -772,7 +772,7 @@ smith-waterman  (writing parameters)
       info for 37 / 37 = 1.000   (removed: 0 failed)
       kept 1 (0.027) unproductive
         writing sw results to test/paired/new-results/test/parameters/data/igk/sw-cache.yaml
-    writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.4 sec)
+    writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.3 sec)
     water time: 1.5  (ig-sw 1.4  processing 0.1)
   writing hmms     removed 0  genes from glfo (leaving v 16  d 1  j 7)
 (1.0 sec)
@@ -780,14 +780,14 @@ hmm
     reading output
         read 37 hmm output lines with 37 sequences in 37 events  (0 failures)
     writing parameters to test/paired/new-results/test/parameters/data/igk/hmm (1.3 sec)
-         infra time: 1.4
+         infra time: 1.3
       hmm step time: 1.9
   writing hmms     removed 0  genes from glfo (leaving v 16  d 1  j 7)
-(1.0 sec)
+(1.1 sec)
       total time: 5.7
 [44mcache-parameters[0m [94migl[0m:
-[91mrun[0m partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/749815/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/749815/meta.yaml
-  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
+[91mrun[0m partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/888813/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/888813/meta.yaml
+  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/888813/meta.yaml: paired-uids
 caching parameters
   vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.0 sec
     keeping 10 / 80 v genes
@@ -814,5 +814,199 @@ hmm
   writing hmms     removed 0  genes from glfo (leaving v 10  d 1  j 3)
 (0.6 sec)
       total time: 3.5
-      [93mwarning[0m expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/749815/: failed.fa
-      total time: 21.8
+      [93mwarning[0m expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/888813/: failed.fa
+      total time: 22.1
+[92msimulate[0m                         partis simulate --dont-write-git-info --paired-loci --parameter-dir test/paired/new-results/test/parameters/data --n-sim-events 10 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/test/simu --indel-frequency 0.2
+[94migh+igk[0m: simulating 7 events
+[44mgenerate-trees[0m [94migh+igk[0m:[94m igh[0m
+[91mrun[0m partis simulate --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-trees 7 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 2003260051 --indel-frequency 0.2 --generate-trees --outfname test/paired/new-results/test/simu/igh+igk/trees.nwk
+  note: reducing --n-procs to 1 (was 4) so it isn't bigger than --n-sim-events
+  generating 7 trees, n-leaves from geometric distribution with parameter 5.0
+    mean over 7 trees:   depth 0.02051   leaves 5.57
+    writing trees to test/paired/new-results/test/simu/igh+igk/trees.nwk
+      total time: 1.3
+[44msimulate[0m [94migh+igk[0m:[94m igh[0m
+[91mrun[0m partis simulate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-sim-events 7 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 2003260051 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igk/igh.yaml --input-simulation-treefname test/paired/new-results/test/simu/igh+igk/trees.nwk
+  note: reducing --n-procs to 7 (was 10) so it isn't bigger than --n-sim-events
+simulating
+      --> proc 0
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 12 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 1
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 seqs in 0.2s (0.0s of which was running bppseqgen)
+      total time: 0.2
+      --> proc 2
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-2.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 3
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-3.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 2 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 4
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-4.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 5
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-5.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 9 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 6
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-6.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 8 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+   read 7 events with 39 seqs from 7 .yaml files
+      total time: 4.1
+[44msimulate[0m [94migh+igk[0m:[94m igk[0m
+[91mrun[0m partis simulate --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igk --n-sim-events 7 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 2077655082 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igk/igk.yaml --input-simulation-treefname test/paired/new-results/test/simu/igh+igk/trees.nwk
+  note: reducing --n-procs to 7 (was 10) so it isn't bigger than --n-sim-events
+simulating
+      --> proc 0
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 12 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 1
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 2
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-2.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 3
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-3.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 4
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-4.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.0
+      --> proc 5
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-5.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 9 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.2
+      --> proc 6
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-6.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 8 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+   read 7 events with 39 seqs from 7 .yaml files
+      total time: 4.1
+[94migh+igl[0m: simulating 3 events
+[44mgenerate-trees[0m [94migh+igl[0m:[94m igh[0m
+[91mrun[0m partis simulate --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-trees 3 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 982264879 --indel-frequency 0.2 --generate-trees --outfname test/paired/new-results/test/simu/igh+igl/trees.nwk
+  note: reducing --n-procs to 1 (was 4) so it isn't bigger than --n-sim-events
+  generating 3 trees, n-leaves from geometric distribution with parameter 5.0
+    mean over 3 trees:   depth 0.05242   leaves 9.00
+    writing trees to test/paired/new-results/test/simu/igh+igl/trees.nwk
+      total time: 1.3
+[44msimulate[0m [94migh+igl[0m:[94m igh[0m
+[91mrun[0m partis simulate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-sim-events 3 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 982264879 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igl/igh.yaml --input-simulation-treefname test/paired/new-results/test/simu/igh+igl/trees.nwk
+  note: reducing --n-procs to 3 (was 10) so it isn't bigger than --n-sim-events
+simulating
+      --> proc 0
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/99260/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 14 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 1
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/99260/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 2
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/99260/trees-sub-2.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+   read 3 events with 27 seqs from 3 .yaml files
+      total time: 2.0
+[44msimulate[0m [94migh+igl[0m:[94m igl[0m
+[91mrun[0m partis simulate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igl --n-sim-events 3 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 1083609742 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igl/igl.yaml --input-simulation-treefname test/paired/new-results/test/simu/igh+igl/trees.nwk
+  note: reducing --n-procs to 3 (was 10) so it isn't bigger than --n-sim-events
+simulating
+      --> proc 0
+    reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/63603/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 14 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+      --> proc 1
+    reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/63603/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.0
+      --> proc 2
+    reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/63603/trees-sub-2.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 10 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.0
+   read 3 events with 27 seqs from 3 .yaml files
+      total time: 2.2
+[94migh+igk[0m: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igk/
+[94migh+igl[0m: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igl/
+  concatenating heavy chain loci:
+      [94mh[0m starting with 7 annotations (39 seqs)
+      [95mk[0m starting with 7 annotations (39 seqs)
+      [94mh[0m adding 3 annotations (27 seqs) for total 7 (39)
+      [92ml[0m starting with 3 annotations (27 seqs)
+    finished with:
+     [94mh[0m: 10 annotations (66 seqs)
+  apportioned 132 seqs among 52 droplets (mean/2 1.3): 4 2 2 2 2 4 2 2 2 2 2 2 4 2 2 2 4 4 2 2 4 2 2 2 2 2 2 4 2 2 4 2 4 2 2 2 2 2 2 2 2 2 4 4 2 4 2 2 2 4 4 2
+  removed 19 / 132 = 0.14 seqs from outfos (leaving 7 / 113 unpaired)
+    writing combined h/l info to fasta and meta files in test/paired/new-results/test/simu
+      total time: 22.8