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

test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.016,0.0,,0.0
+0.0,1.0,,0.03717459069360163
+0.016,1.0,,0.12831445712826428
+0.032,0.0,,0.0
+0.048,0.0,,0.0
+0.064,0.0,,0.0
+0.08,0.0,,0.0
+0.096,0.0,,0.0
+0.112,0.0,,0.0
+0.128,0.0,,0.0
+0.14400000000000002,0.0,,0.0
+0.16,0.0,,0.0
+0.176,0.0,,0.0
+0.192,0.0,,0.0
+0.20800000000000002,0.0,,0.0
+0.224,0.0,,0.0
+0.24,0.0,,0.0
+0.256,0.0,,0.0
+0.272,0.0,,0.0
+0.28800000000000003,0.0,,0.0
+0.304,0.0,,0.0
+0.32,0.0,,0.0
+0.336,0.0,,0.0
+0.352,0.0,,0.0
+0.368,0.0,,0.0
+0.384,0.0,,0.0
+0.4,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_gene.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,1.0,right,0.030056064897528434
+0.5,0.0,wrong,0.066735136327
+1.5,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv

@@ -0,0 +1,6 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,31.0,,5.5677643628300215
+0.5,3,,1.7320508075688772
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv

@@ -0,0 +1,7 @@
+bin_low_edge,contents,binlabel,error
+-2.5,0.0,,0.0
+-1.5,2.0,,1.4142135623730951
+-0.5,31,,5.5677643628300215
+0.5,1,,1.0
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,34.0,,5.830951894845301
+0.5,1.0,,1.0
+1.5,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-2.5,0.0,,0.0
+-1.5,1.0,,1.0
+-0.5,34.0,,5.830951894845301
+0.5,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv

@@ -0,0 +1,6 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,31.0,,5.5677643628300215
+0.5,3,,1.7320508075688772
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv

@@ -0,0 +1,6 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,33.0,,5.744562646538029
+0.5,1,,1.0
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freqs.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.0432,0.0,,0.0
+-0.04,0.0,,0.0
+-0.0368,0.0,,0.0
+-0.0336,0.0,,0.0
+-0.0304,0.0,,0.0
+-0.027200000000000002,0.0,,0.0
+-0.024,0.0,,0.0
+-0.0208,0.0,,0.0
+-0.0176,0.0,,0.0
+-0.0144,0.0,,0.0
+-0.011199999999999998,0.0,,0.0
+-0.008,0.0,,0.0
+-0.004799999999999999,2.0,,1.4142135623730951
+-0.0015999999999999973,31.0,,5.5677643628300215
+0.0016000000000000042,1.0,,1.0
+0.004799999999999999,1.0,,1.0
+0.008,0.0,,0.0
+0.011200000000000002,0.0,,0.0
+0.014400000000000003,0.0,,0.0
+0.017600000000000005,0.0,,0.0
+0.0208,0.0,,0.0
+0.024,0.0,,0.0
+0.02720000000000001,0.0,,0.0
+0.030400000000000003,0.0,,0.0
+0.0336,0.0,,0.0
+0.036800000000000006,0.0,,0.0
+0.04,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv

@@ -0,0 +1,7 @@
+bin_low_edge,contents,binlabel,error
+-2.5,0.0,,0.0
+-1.5,2.0,,1.4142135623730951
+-0.5,31,,5.5677643628300215
+0.5,1,,1.0
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/partition-new-simu.yaml

@@ -0,0 +1 @@
+{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": -Infinity, "n_clusters": 12, "n_procs": 2, "partition": [["162cb1691f", "17f57acf2e", "73431a9b10", "73d6c6e558", "948b83fb4d", "bf50fa2017", "c8a90cc3d7"], ["16df39683f", "7f6d2ba874"], ["188e1a0235", "226be79d5f"], ["401a542698"], ["93c01dd961", "c761732a8b"], ["d8761c689a"], ["13de8675ec", "20a0129b57", "31e052ee14", "33aaa62e12", "4233d708fe", "91796617a0", "97366cf0d8"], ["18f4019708", "308de1d739", "5fb484a8a6", "648902c3e5", "8024ed1a22", "822801f8ab", "d024e5cab0", "ee25049b92", "efdea248af", "f47122f1f5"], ["6e208eca11"], ["9c3cedb840"], ["adc41b4237"], ["e64fcd9e03"]], "ccf_under": 0.911111111111111, "ccf_over": 0.8649691358024691, "perf_metrics": {}, "n_true_clusters": 10}, {"logprob": -2286.8870677439777, "n_clusters": 11, "n_procs": 1, "partition": [["13de8675ec", "20a0129b57", "31e052ee14", "33aaa62e12", "4233d708fe", "91796617a0", "97366cf0d8"], ["162cb1691f", "17f57acf2e", "73431a9b10", "73d6c6e558", "948b83fb4d", "bf50fa2017", "c8a90cc3d7"], ["16df39683f", "7f6d2ba874"], ["188e1a0235", "226be79d5f"], ["18f4019708", "308de1d739", "5fb484a8a6", "648902c3e5", "8024ed1a22", "822801f8ab", "d024e5cab0", "ee25049b92", "efdea248af", "f47122f1f5", "9c3cedb840"], ["401a542698"], ["6e208eca11"], ["93c01dd961", "c761732a8b"], ["adc41b4237"], ["d8761c689a"], ["e64fcd9e03"]], "ccf_under": 0.9090909090909087, "ccf_over": 0.9143518518518517, "perf_metrics": {}, "n_true_clusters": 10}, {"logprob": -2235.642663617658, "n_clusters": 10, "n_procs": 1, "partition": [["13de8675ec", "20a0129b57", "31e052ee14", "33aaa62e12", "4233d708fe", "91796617a0", "97366cf0d8"], ["162cb1691f", "17f57acf2e", "73431a9b10", "73d6c6e558", "948b83fb4d", "bf50fa2017", "c8a90cc3d7"], ["16df39683f", "7f6d2ba874", "6e208eca11"], ["188e1a0235", "226be79d5f"], ["18f4019708", "308de1d739", "5fb484a8a6", "648902c3e5", "8024ed1a22", "822801f8ab", "d024e5cab0", "ee25049b92", "efdea248af", "f47122f1f5", "9c3cedb840"], ["401a542698"], ["93c01dd961", "c761732a8b"], ["adc41b4237"], ["d8761c689a"], ["e64fcd9e03"]], "ccf_under": 0.9090909090909087, "ccf_over": 0.9513888888888888, "perf_metrics": {}, "n_true_clusters": 10}], "events": [{"has_shm_indels": [false, false, false, false, false, false, false, false, false, false, false], "qr_gap_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "gl_gap_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "indel_reversed_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "unique_ids": ["18f4019708", "308de1d739", "5fb484a8a6", "648902c3e5", "8024ed1a22", "822801f8ab", "d024e5cab0", "ee25049b92", "efdea248af", "f47122f1f5", "9c3cedb840"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mut_freqs": [0.02023121387283237, 0.017341040462427744, 0.02023121387283237, 0.011560693641618497, 0.011560693641618497, 0.0, 0.0, 0.023121387283236993, 0.014450867052023121, 0.011560693641618497, 0.02023121387283237], "n_mutations": [7, 6, 7, 4, 4, 0, 0, 8, 5, 4, 7], "input_seqs": ["NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGACGGCTTGGTCCAGCCTGGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGGGCTGGGTCCGCCAGGCTCCAAGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTGAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTTTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTATCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGGGTATTACTGTGCGAGATCTATCGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCTTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTCGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGACACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCTGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACGTGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGTCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999990466130269, "IGHD6-19*01": 9.533869773964565e-07}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "C", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true, true, true], "stops": [true, true, true, true, true, false, false, true, true, true, true], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 318}}, {"has_shm_indels": [false, false, true, true, false, false, false], "qr_gap_seqs": ["", "", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "gl_gap_seqs": ["", "", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGG...CTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGC.......TGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "indel_reversed_seqs": ["", "", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "unique_ids": ["13de8675ec", "20a0129b57", "31e052ee14", "33aaa62e12", "4233d708fe", "91796617a0", "97366cf0d8"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mut_freqs": [0.0, 0.0027247956403269754, 0.0, 0.0, 0.0, 0.0, 0.0027247956403269754], "n_mutations": [0, 1, 0, 0, 0, 0, 1], "input_seqs": ["NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTAGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTTCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV1-18*01": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999999999994316, "IGHD6-19*01": 5.698073919757748e-13}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 5, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCCTCGCA", "dj_insertion": "TCCCT", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true], "stops": [false, false, false, false, false, false, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 336}}, {"has_shm_indels": [false, false, false, true, false, false, false], "qr_gap_seqs": ["", "", "", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGT.......CTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATG.....AGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", ""], "gl_gap_seqs": ["", "", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", ""], "indel_reversed_seqs": ["", "", "", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", ""], "unique_ids": ["162cb1691f", "17f57acf2e", "73431a9b10", "73d6c6e558", "948b83fb4d", "bf50fa2017", "c8a90cc3d7"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 60, "mut_freqs": [0.0158311345646438, 0.013192612137203167, 0.013192612137203167, 0.010554089709762533, 0.010554089709762533, 0.0079155672823219, 0.018469656992084433], "n_mutations": [6, 5, 5, 4, 4, 3, 7], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTAATACGAATACTTCCAGCACTGGGGCCAGGGCATCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGATTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGTACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAATTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGAGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAATCCTTCGGAGAGCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTAGTACAGTGGGAGCACCAACTACAACCCCTCCCTCAATAGTGGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCAGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV4-61*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ1*01": 1.0}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 3, "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, true, true, true], "stops": [true, true, false, false, false, false, true], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 345}}, {"has_shm_indels": [false, false, false], "qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["16df39683f", "7f6d2ba874", "6e208eca11"], "invalid": false, "v_gene": "IGHV3-7*05", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ6*02", "cdr3_length": 63, "mut_freqs": [0.0158311345646438, 0.010554089709762533, 0.023746701846965697], "n_mutations": [6, 4, 9], "input_seqs": ["NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTAAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGGGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATATTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGATCCGAAGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATGTTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGCGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAAGGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATATTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTGTATTACTGTGCTAGAGACTGCGAAGCAGCTGGTACCTGTTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGACAAGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGHV3-7*05": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999999030671394, "IGHD6-19*01": 9.69328761020389e-08}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 0, "j_5p_del": 17, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CTGCGA", "dj_insertion": "CTATTCTAAGTTGCGTGAG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [true, true, true], "loci": ["igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 348}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["188e1a0235", "226be79d5f"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD3-16*02", "j_gene": "IGHJ4*02", "cdr3_length": 54, "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-23*01": 1.0}, "d_per_gene_support": {"IGHD3-16*02": 1.0}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "loci": ["igh", "igh"], "codon_positions": {"v": 288, "j": 339}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["93c01dd961", "c761732a8b"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD1-20*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mut_freqs": [0.002840909090909091, 0.005681818181818182], "n_mutations": [1, 2], "input_seqs": ["NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGGATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACAAGGCTGTGGATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD1-20*01": 1.0}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "AGTATG", "dj_insertion": "TCTCAGA", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "loci": ["igh", "igh"], "codon_positions": {"v": 288, "j": 324}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["401a542698"], "invalid": false, "v_gene": "IGHV4-4*09", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mut_freqs": [0.013850415512465374], "n_mutations": [5], "input_seqs": ["NNNNNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTACTTACTACTGGAGCTGGATCCGGCAGTCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCAAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGTAGCAGAGCCCCTGTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGCAGCAGAGCCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-4*09": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999996029153599, "IGHD6-19*01": 3.9708463321213133e-07}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 3, "d_5p_del": 0, "d_3p_del": 7, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTATTTGCTC", "dj_insertion": "AGCCCC", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "loci": ["igh"], "codon_positions": {"v": 288, "j": 333}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["adc41b4237"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mut_freqs": [0.013513513513513514], "n_mutations": [5], "input_seqs": ["NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTGCATGAGCTGGGTCCGCCAGGCTCCACGGGAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAAGACGCTGTATCTTCAAATGAACAGCCTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999999913297444, "IGHD6-19*01": 8.670260428895021e-09}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 7, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTTTTGTGTCGGCAGGA", "dj_insertion": "GGCGCCC", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "loci": ["igh"], "codon_positions": {"v": 288, "j": 342}}, {"has_shm_indels": [true], "qr_gap_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACC............AGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "unique_ids": ["d8761c689a"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 64, "mut_freqs": [0.020887728459530026], "n_mutations": [8], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-61*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ1*01": 1.0}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GAATACT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [false], "loci": ["igh"], "codon_positions": {"v": 288, "j": 349}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["e64fcd9e03"], "invalid": false, "v_gene": "IGHV5-51*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mut_freqs": [0.01098901098901099], "n_mutations": [4], "input_seqs": ["NNNGAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGGGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTCTCCTGGTGACTCTGATGCCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGACTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV5-51*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9816252828850575, "IGHD6-13*01": 0.018374717114945146}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 1, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TA", "dj_insertion": "TCG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "loci": ["igh"], "codon_positions": {"v": 288, "j": 333}}]}

test/new-results/run-times.csv

@@ -0,0 +1,10 @@
+name,seconds
+cache-parameters-simu,5.2
+annotate-new-simu,2.0
+multi-annotate-new-simu,1.8
+partition-new-simu,3.0
+seed-partition-new-simu,1.6
+vsearch-partition-new-simu,1.9
+get-selection-metrics-new-simu,1.4
+cache-parameters-data,6.2
+simulate,12.7

test/new-results/seed-partition-new-simu.yaml

@@ -0,0 +1 @@
+{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": 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"qr_gap_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "gl_gap_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "indel_reversed_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "unique_ids": ["18f4019708", "308de1d739", "5fb484a8a6", "648902c3e5", "8024ed1a22", "822801f8ab", "d024e5cab0", "ee25049b92", "efdea248af", "f47122f1f5", "9c3cedb840"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mut_freqs": [0.02023121387283237, 0.017341040462427744, 0.02023121387283237, 0.011560693641618497, 0.011560693641618497, 0.0, 0.0, 0.023121387283236993, 0.014450867052023121, 0.011560693641618497, 0.02023121387283237], "n_mutations": [7, 6, 7, 4, 4, 0, 0, 8, 5, 4, 7], "input_seqs": ["NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGACGGCTTGGTCCAGCCTGGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGGGCTGGGTCCGCCAGGCTCCAAGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTGAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTTTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTATCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGGGTATTACTGTGCGAGATCTATCGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCTTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTCGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGACACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCTGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACGTGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGTCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999990466130269, "IGHD6-19*01": 9.533869773964565e-07}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "C", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true, true, true], "stops": [true, true, true, true, true, false, false, true, true, true, true], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 318}}]}

test/new-results/test/parameters/data/hmm/all-mean-mute-freqs.csv

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test/new-results/test/parameters/data/hmm/all-mean-n-muted.csv

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test/new-results/test/parameters/data/hmm/all-probs.csv

@@ -0,0 +1,44 @@
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+IGHV3-23*01,IGHD6-13*01,IGHJ4*02,0,0,8,3,4,0,3,9,2,0,45,1
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+IGHV4-39*09,IGHD3-10*01,IGHJ4*02,0,1,5,10,4,0,0,5,10,0,54,1
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+IGHV4-4*09,IGHD6-13*01,IGHJ4*02,0,3,0,7,10,0,6,10,9,0,48,1
+IGHV2-70D*04,IGHD4-4*01,IGHJ6*02,0,4,3,5,19,0,0,4,8,0,42,1
+IGHV3-66*02,IGHD1-20*01,IGHJ4*02,0,2,3,7,8,0,6,6,8,0,39,2
+IGHV3-9*02,IGHD3-10*03,IGHJ5*02,0,0,9,9,9,0,3,15,5,0,57,1
+IGHV1-2*02,IGHD2-15*01,IGHJ4*02,0,2,2,3,13,0,3,1,41,0,81,1
+IGHV3-66*02,IGHD4-4*01,IGHJ4*02,0,2,0,7,14,0,6,1,11,0,33,1
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+IGHV2-5*02,IGHD3-10*01,IGHJ4*02,0,3,12,3,7,0,0,21,9,0,66,1
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+IGHV1-2*02,IGHD2-8*01,IGHJ4*02,0,1,0,0,0,0,3,1,22,0,81,1
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+IGHV3-11*04,IGHD6-13*01,IGHJ4*02,0,4,1,1,7,0,3,5,16,0,57,1
+IGHV1-2*02,IGHD3-16*02,IGHJ2*01,0,1,3,0,0,0,3,6,9,0,81,1
+IGHV3-69-1*02,IGHD1-26*01,IGHJ4*02,0,0,10,3,4,0,6,14,3,0,48,1
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+IGHV1-2*02,IGHD2-15*01,IGHJ2*01,0,1,0,3,2,0,3,1,1,0,60,1
+IGHV4-34*01,IGHD3-10*01,IGHJ4*02,0,1,2,9,6,0,6,10,6,0,57,1
+IGHV3-69-1*02,IGHD2-8*02,IGHJ4*02,0,2,10,13,4,0,6,11,4,0,45,1
+IGHV3-23*01,IGHD3-22*01,IGHJ4*02,0,6,12,10,12,0,3,15,8,0,42,1
+IGHV3-7*05,IGHD6-13*01,IGHJ6*02,0,0,9,0,17,0,3,6,19,0,63,1
+IGHV3-69-1*02,IGHD6-6*01,IGHJ3*02,0,0,7,0,0,0,6,13,6,0,60,1
+IGHV3-11*04,IGHD6-6*01,IGHJ3*02,0,0,2,0,0,0,3,6,2,0,54,1
+IGHV1-18*01,IGHD6-13*01,IGHJ4*02,0,0,2,7,6,0,3,9,8,0,51,1
+IGHV3-69-1*02,IGHD2-15*01,IGHJ4*02,0,2,3,5,12,0,6,5,3,0,45,1
+IGHV3-23*01,IGHD2-21*01,IGHJ5*02,0,0,1,11,2,0,3,19,9,0,73,1
+IGHV3-23*01,IGHD2-2*01,IGHJ5*02,0,0,17,5,6,0,3,6,2,0,42,1
+IGHV4-61*01,IGHD3-22*01,IGHJ1*01,0,0,0,0,3,0,0,0,0,0,60,1

test/new-results/test/parameters/data/hmm/cluster_size.csv

@@ -0,0 +1,2 @@
+cluster_size,count
+1,46

test/new-results/test/parameters/data/hmm/d-mean-mute-freqs.csv

@@ -0,0 +1,43 @@
+bin_low_edge,contents,binlabel,error
+-0.01,0.0,,0.0
+0.0,0.391304347826087,,0.09223131928520184
+0.01,0.0,,0.0
+0.02,0.0,,0.0
+0.03,0.0,,0.0
+0.04,0.0,,0.0
+0.05,0.0,,0.0
+0.06,0.06521739130434782,,0.03765327842541037
+0.07,0.021739130434782608,,0.021739130434782608
+0.08,0.043478260869565216,,0.030743773095067286
+0.09,0.0,,0.0
+0.1,0.06521739130434782,,0.03765327842541037
+0.11,0.043478260869565216,,0.030743773095067286
+0.12,0.0,,0.0
+0.13,0.0,,0.0
+0.14,0.043478260869565216,,0.030743773095067286
+0.15,0.0,,0.0
+0.16,0.043478260869565216,,0.030743773095067286
+0.17,0.021739130434782608,,0.021739130434782608
+0.18,0.021739130434782608,,0.021739130434782608
+0.19,0.0,,0.0
+0.2,0.0,,0.0
+0.21,0.021739130434782608,,0.021739130434782608
+0.22,0.0,,0.0
+0.23,0.021739130434782608,,0.021739130434782608
+0.24,0.0,,0.0
+0.25,0.0,,0.0
+0.26,0.0,,0.0
+0.27,0.0,,0.0
+0.28,0.021739130434782608,,0.021739130434782608
+0.29,0.0,,0.0
+0.3,0.021739130434782608,,0.021739130434782608
+0.31,0.0,,0.0
+0.32,0.043478260869565216,,0.030743773095067286
+0.33,0.0,,0.0
+0.34,0.0,,0.0
+0.35000000000000003,0.043478260869565216,,0.030743773095067286
+0.36,0.0,,0.0
+0.37,0.0,,0.0
+0.38,0.021739130434782608,,0.021739130434782608
+0.39,0.0,,0.0
+0.4,0.043478260869565216,,0.030743773095067286

test/new-results/test/parameters/data/hmm/d-mean-n-muted.csv

@@ -0,0 +1,14 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,18.0,,4.242640687119285
+0.5,9.0,,3.0
+1.5,6.0,,2.449489742783178
+2.5,1.0,,1.0
+3.5,1.0,,1.0
+4.5,3.0,,1.7320508075688772
+5.5,3.0,,1.7320508075688772
+6.5,0.0,,0.0
+7.5,0.0,,0.0
+8.5,0.0,,0.0
+9.5,2.0,,1.4142135623730951
+10.5,3.0,,1.7320508075688772

test/new-results/test/parameters/data/hmm/d_gene-d_3p_del-probs.csv

@@ -0,0 +1,34 @@
+d_3p_del,d_gene,count
+2,IGHD6-13*01,1
+3,IGHD6-13*01,1
+0,IGHD2-8*01,3
+1,IGHD4-17*01,1
+8,IGHD3-3*01,1
+6,IGHD6-13*01,3
+10,IGHD3-10*01,1
+0,IGHD3-16*02,3
+7,IGHD6-6*01,1
+7,IGHD6-13*01,2
+5,IGHD4-4*01,1
+7,IGHD1-20*01,2
+9,IGHD3-10*03,1
+3,IGHD2-15*01,3
+7,IGHD4-4*01,1
+0,IGHD6-13*01,2
+3,IGHD3-10*01,1
+6,IGHD6-6*01,1
+0,IGHD2-15*01,1
+0,IGHD5-5*01,2
+0,IGHD6-19*01,1
+2,IGHD4-17*01,1
+0,IGHD2-21*02,1
+1,IGHD6-13*01,1
+3,IGHD1-26*01,1
+9,IGHD3-10*01,1
+13,IGHD2-8*02,1
+10,IGHD3-22*01,1
+0,IGHD6-6*01,2
+5,IGHD2-15*01,1
+11,IGHD2-21*01,1
+5,IGHD2-2*01,1
+0,IGHD3-22*01,1