partis-bcr 1.0.11__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev1__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 (43) hide show
  1. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev1.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev1.dist-info}/RECORD +43 -43
  3. test/new-results/test.log +1 -1
  4. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  5. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +5 -5
  6. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +1 -1
  7. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +3 -3
  8. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  9. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  10. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  11. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  23. test/paired/new-results/run-times.csv +4 -4
  24. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +4 -8
  25. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +5 -9
  26. test/paired/new-results/subset-partition-new-simu/merged-partition.log +2 -6
  27. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  28. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  29. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  30. test/paired/new-results/test.log +31 -40
  31. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  32. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  33. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  34. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  35. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev1.data}/scripts/gctree-run.py +0 -0
  36. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  37. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev1.data}/scripts/parse-output.py +0 -0
  38. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev1.data}/scripts/partis-test.py +0 -0
  39. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev1.data}/scripts/split-loci.py +0 -0
  40. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev1.dist-info}/WHEEL +0 -0
  41. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev1.dist-info}/entry_points.txt +0 -0
  42. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev1.dist-info}/licenses/COPYING +0 -0
  43. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev1.dist-info}/top_level.txt +0 -0
test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml CHANGED
@@ -1 +1 @@
1
- {"version-info": {"partis-yaml": 0.1, "partis-git": {"commit": "b1783efdc4bea09eb047e057f603af1558441dcb", "tag": "v1.0.11"}}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ2*01": "TGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ4*01": "TTTTGTATTTGGTGGAGGAACCCAGCTGATCATTTTAG", "IGLJ5*01": "CTGGGTGTTTGGTGAGGGGACCGAGCTGACCGTCCTAG", "IGLJ5*02": "CTGGGTGTTTGGTGAGGGGACGGAGCTGACCGTCCTAG", "IGLJ6*01": "TAATGTGTTCGGCAGTGGCACCAAGGTGACCGTCCTCG", "IGLJ7*01": "TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGTCCTCG", "IGLJ7*02": "TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGCCCTCG"}}, "cyst-positions": {"IGLV2-14*04": 267, "IGLV2-23*02": 267, "IGLV1-40*01": 267}, "phen-positions": {"IGLJ5*02": 7, "IGLJ5*01": 7, "IGLJ6*01": 7, "IGLJ7*01": 7, "IGLJ7*02": 7, "IGLJ1*01": 7, "IGLJ2*01": 7, "IGLJ4*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": 0.0, "n_clusters": 21, "n_procs": 1, "partition": [["253ca59333-igl"], ["b739ce37b7-igl"], ["aa25e6c0ce-igl"], ["7588f09c07-igl"], ["8807c8ff04-igl"], ["20909c3943-igl"], ["a3baa83300-igl"], ["971ac047ee-igl"], ["a2238f4e9a-igl"], ["8d79fca804-igl"], ["0eb272ee70-igl"], ["09f5010bd3-igl"], ["b02ee7754a-igl"], ["ddcf0ca433-igl"], ["eee6809ad6-igl"], ["14195e4958-igl"], ["d5ddf0c2ec-igl"], ["57537e5f22-igl"], ["b1e56e40a1-igl"], ["21cea6e4d0-igl"], ["4d37fe487e-igl"]]}], "events": [{"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["253ca59333-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.014970059880239521], "n_mutations": [5], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["253ca59333-igh", "b739ce37b7-igh", "b739ce37b7-igl"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1445, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["b739ce37b7-igl"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["253ca59333-igh", "253ca59333-igl", "b739ce37b7-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 297}, "k_v": {"best": 288, "min": 285, "max": 289}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-23*02": {"score": 1440, "glbounds": [0, 288], "qrbounds": [0, 288]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [288, 288]}}, "j": {"IGLJ1*01": {"score": 190, "glbounds": [0, 38], "qrbounds": [290, 328]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["aa25e6c0ce-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.029940119760479042], "n_mutations": [10], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTCGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGAACCTCCGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTGCTGCCAGTCCTTTGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["aa25e6c0ce-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1395, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["7588f09c07-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCACAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTAATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["7588f09c07-igh", "cb8a759f1a-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["8807c8ff04-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["a4b090d0be-igh", "a4b090d0be-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["20909c3943-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [[]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["a3baa83300-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.02694610778443114], "n_mutations": [9], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCGTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["a3baa83300-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1405, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATC.GCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "unique_ids": ["971ac047ee-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [true], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [true], "paired-uids": [["c0fcfe005f-igh", "c0fcfe005f-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["a2238f4e9a-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.020958083832335328], "n_mutations": [7], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCGCCAAGTCTGGCACCTCGGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["a2238f4e9a-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1425, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["8d79fca804-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.029940119760479042], "n_mutations": [10], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCGTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCGAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["8d79fca804-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1395, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["0eb272ee70-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.029940119760479042], "n_mutations": [10], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACAGCGGGGCAGGTTATGATGTAAACTGGTACCAGCTGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGTCCATCACAGGGCTCCAGGTAGAGGATGAGGCTGATTATTACTGCAAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["0eb272ee70-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1395, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["09f5010bd3-igl"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["09f5010bd3-igh", "cfe3b29587-igh", "cfe3b29587-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 297}, "k_v": {"best": 288, "min": 285, "max": 289}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-23*02": {"score": 1440, "glbounds": [0, 288], "qrbounds": [0, 288]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [288, 288]}}, "j": {"IGLJ1*01": {"score": 190, "glbounds": [0, 38], "qrbounds": [290, 328]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["b02ee7754a-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["b02ee7754a-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGAT........TCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "indel_reversed_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "unique_ids": ["ddcf0ca433-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.020958083832335328], "n_mutations": [7], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [true], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [true], "paired-uids": [["ddcf0ca433-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1425, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": ["CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGCCCTG...ACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "unique_ids": ["eee6809ad6-igl"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [true], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["bc11af4843-igh", "bc11af4843-igk", "eee6809ad6-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 297}, "k_v": {"best": 288, "min": 285, "max": 289}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-23*02": {"score": 1440, "glbounds": [0, 288], "qrbounds": [0, 288]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [288, 288]}}, "j": {"IGLJ1*01": {"score": 190, "glbounds": [0, 38], "qrbounds": [290, 328]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCA........GCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "unique_ids": ["14195e4958-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [true], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [true], "paired-uids": [["14195e4958-igh", "d5ddf0c2ec-igl"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["d5ddf0c2ec-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCGGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["14195e4958-igh", "14195e4958-igl"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["57537e5f22-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["57537e5f22-igh", "7ba384a461-igh", "7ba384a461-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["b1e56e40a1-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["b1e56e40a1-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["21cea6e4d0-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["21cea6e4d0-igh", "f094dfd68a-igh", "f094dfd68a-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["4d37fe487e-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.03293413173652695], "n_mutations": [11], "input_seqs": ["TAGTCTGTGCAGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTAGGAGCAGCTCCAACATCGGTGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCATGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGCTGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["4d37fe487e-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1385, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}]}
1
+ {"version-info": {"partis-yaml": 0.1, "partis-git": {"commit": "dcad8ab09973ffc29295e5ed3660d4c5ae633b28", "tag": "v1.0.11", "n_ahead_of_tag": "1"}}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ2*01": "TGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ4*01": "TTTTGTATTTGGTGGAGGAACCCAGCTGATCATTTTAG", "IGLJ5*01": "CTGGGTGTTTGGTGAGGGGACCGAGCTGACCGTCCTAG", "IGLJ5*02": "CTGGGTGTTTGGTGAGGGGACGGAGCTGACCGTCCTAG", "IGLJ6*01": "TAATGTGTTCGGCAGTGGCACCAAGGTGACCGTCCTCG", "IGLJ7*01": "TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGTCCTCG", "IGLJ7*02": "TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGCCCTCG"}}, "cyst-positions": {"IGLV2-14*04": 267, "IGLV2-23*02": 267, "IGLV1-40*01": 267}, "phen-positions": {"IGLJ5*02": 7, "IGLJ5*01": 7, "IGLJ6*01": 7, "IGLJ7*01": 7, "IGLJ7*02": 7, "IGLJ1*01": 7, "IGLJ2*01": 7, "IGLJ4*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": 0.0, "n_clusters": 21, "n_procs": 1, "partition": [["253ca59333-igl"], ["b739ce37b7-igl"], ["aa25e6c0ce-igl"], ["7588f09c07-igl"], ["8807c8ff04-igl"], ["20909c3943-igl"], ["a3baa83300-igl"], ["971ac047ee-igl"], ["a2238f4e9a-igl"], ["8d79fca804-igl"], ["0eb272ee70-igl"], ["09f5010bd3-igl"], ["b02ee7754a-igl"], ["ddcf0ca433-igl"], ["eee6809ad6-igl"], ["14195e4958-igl"], ["d5ddf0c2ec-igl"], ["57537e5f22-igl"], ["b1e56e40a1-igl"], ["21cea6e4d0-igl"], ["4d37fe487e-igl"]]}], "events": [{"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["253ca59333-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.014970059880239521], "n_mutations": [5], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["253ca59333-igh", "b739ce37b7-igh", "b739ce37b7-igl"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1445, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["b739ce37b7-igl"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["253ca59333-igh", "253ca59333-igl", "b739ce37b7-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 297}, "k_v": {"best": 288, "min": 285, "max": 289}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-23*02": {"score": 1440, "glbounds": [0, 288], "qrbounds": [0, 288]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [288, 288]}}, "j": {"IGLJ1*01": {"score": 190, "glbounds": [0, 38], "qrbounds": [290, 328]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["aa25e6c0ce-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.029940119760479042], "n_mutations": [10], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTCGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGAACCTCCGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTGCTGCCAGTCCTTTGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["aa25e6c0ce-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1395, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["7588f09c07-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCACAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTAATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["7588f09c07-igh", "cb8a759f1a-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["8807c8ff04-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["a4b090d0be-igh", "a4b090d0be-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["20909c3943-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [[]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["a3baa83300-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.02694610778443114], "n_mutations": [9], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCGTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["a3baa83300-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1405, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATC.GCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "unique_ids": ["971ac047ee-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [true], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [true], "paired-uids": [["c0fcfe005f-igh", "c0fcfe005f-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["a2238f4e9a-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.020958083832335328], "n_mutations": [7], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCGCCAAGTCTGGCACCTCGGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["a2238f4e9a-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1425, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["8d79fca804-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.029940119760479042], "n_mutations": [10], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCGTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCGAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["8d79fca804-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1395, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["0eb272ee70-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.029940119760479042], "n_mutations": [10], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACAGCGGGGCAGGTTATGATGTAAACTGGTACCAGCTGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGTCCATCACAGGGCTCCAGGTAGAGGATGAGGCTGATTATTACTGCAAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["0eb272ee70-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1395, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["09f5010bd3-igl"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["09f5010bd3-igh", "cfe3b29587-igh", "cfe3b29587-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 297}, "k_v": {"best": 288, "min": 285, "max": 289}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-23*02": {"score": 1440, "glbounds": [0, 288], "qrbounds": [0, 288]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [288, 288]}}, "j": {"IGLJ1*01": {"score": 190, "glbounds": [0, 38], "qrbounds": [290, 328]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["b02ee7754a-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["b02ee7754a-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGAT........TCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "indel_reversed_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "unique_ids": ["ddcf0ca433-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.020958083832335328], "n_mutations": [7], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [true], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [true], "paired-uids": [["ddcf0ca433-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1425, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": ["CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGCCCTG...ACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "unique_ids": ["eee6809ad6-igl"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [true], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["bc11af4843-igh", "bc11af4843-igk", "eee6809ad6-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 297}, "k_v": {"best": 288, "min": 285, "max": 289}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-23*02": {"score": 1440, "glbounds": [0, 288], "qrbounds": [0, 288]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [288, 288]}}, "j": {"IGLJ1*01": {"score": 190, "glbounds": [0, 38], "qrbounds": [290, 328]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCA........GCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "unique_ids": ["14195e4958-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [true], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [true], "paired-uids": [["14195e4958-igh", "d5ddf0c2ec-igl"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["d5ddf0c2ec-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCGGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["14195e4958-igh", "14195e4958-igl"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["57537e5f22-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["57537e5f22-igh", "7ba384a461-igh", "7ba384a461-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["b1e56e40a1-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["b1e56e40a1-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["21cea6e4d0-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["21cea6e4d0-igh", "f094dfd68a-igh", "f094dfd68a-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["4d37fe487e-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.03293413173652695], "n_mutations": [11], "input_seqs": ["TAGTCTGTGCAGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTAGGAGCAGCTCCAACATCGGTGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCATGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGCTGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "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": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["4d37fe487e-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1385, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}]}
test/paired/new-results/test.log CHANGED
@@ -21,7 +21,7 @@ smith-waterman (writing parameters)
21
21
  kept 25 (0.446) unproductive
22
22
  writing sw results to test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
23
23
  writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (0.6 sec)
24
- water time: 0.7 (ig-sw 0.6 processing 0.0)
24
+ water time: 0.7 (ig-sw 0.7 processing 0.0)
25
25
  writing hmms removed 16 genes from glfo (leaving v 6 d 18 j 4)
26
26
  (0.5 sec)
27
27
  hmm
@@ -30,9 +30,9 @@ hmm
30
30
  writing parameters to test/paired/new-results/test/parameters/simu/igh/hmm (0.5 sec)
31
31
  writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.5 sec)
32
32
  infra time: 1.1
33
- hmm step time: 2.2
33
+ hmm step time: 2.1
34
34
  writing hmms removed 3 genes from glfo (leaving v 6 d 15 j 4)
35
- (0.4 sec)
35
+ (0.3 sec)
36
36
  total time: 4.0
37
37
  cache-parameters igk:
38
38
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -68,8 +68,8 @@ hmm
68
68
  infra time: 0.9
69
69
  hmm step time: 1.4
70
70
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
71
- (0.4 sec)
72
- total time: 2.7
71
+ (0.3 sec)
72
+ total time: 2.8
73
73
  cache-parameters igl:
74
74
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
75
75
  run partis cache-parameters --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -122,9 +122,9 @@ smith-waterman
122
122
  (0.0 sec)
123
123
  water time: 0.1
124
124
  hmm
125
- caching all 56 naive sequences (1.1s)
125
+ caching all 56 naive sequences (1.0s)
126
126
  collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
127
- 50 clusters with 10 procs (0.5s)
127
+ 50 clusters with 10 procs (0.6s)
128
128
  44 clusters with 7 procs (0.5s)
129
129
  36 clusters with 5 procs (0.4s)
130
130
  31 clusters with 3 procs (0.3s)
@@ -164,7 +164,7 @@ hmm
164
164
  getting annotations for final partition
165
165
  subcluster annotating 6 clusters with steps: (0.3s) (0.1s) (0.1s) plotting performance (0.0 sec)
166
166
 
167
- subcluster annotation time 0.5
167
+ subcluster annotation time 0.4
168
168
  total time: 1.5
169
169
  partition igl:
170
170
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -228,7 +228,6 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
228
228
  joint 0.963 0.594
229
229
  merge time 0.0
230
230
  need to get annotations for 7/15 joint igh clusters
231
- tag: v1.0.11
232
231
  annotate igh+igk: igh
233
232
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
234
233
  run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igh-only-partition.yaml
@@ -246,7 +245,6 @@ hmm
246
245
  subcluster annotation time 0.6
247
246
  total time: 0.6
248
247
  need to get annotations for 13/15 joint igk clusters
249
- tag: v1.0.11
250
248
  annotate igh+igk: igk
251
249
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
252
250
  run partis annotate --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igk.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igk-only-partition.yaml
@@ -288,7 +286,6 @@ hmm
288
286
  joint 1.000 0.611
289
287
  merge time 0.0
290
288
  need to get annotations for 5/8 joint igh clusters
291
- tag: v1.0.11
292
289
  annotate igh+igl: igh
293
290
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
294
291
  run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igh-only-partition.yaml
@@ -306,7 +303,6 @@ hmm
306
303
  subcluster annotation time 0.4
307
304
  total time: 0.5
308
305
  need to get annotations for 8/8 joint igl clusters
309
- tag: v1.0.11
310
306
  annotate igh+igl: igl
311
307
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
312
308
  run partis annotate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igl.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igl-only-partition.yaml
@@ -335,7 +331,7 @@ hmm
335
331
  h 20 --> 23 +3
336
332
  k 6 --> 15 +9
337
333
  l 3 --> 8 +5
338
- total time: 19.9
334
+ total time: 20.0
339
335
  subset-partition-new-simu 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
340
336
  note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
341
337
  --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -364,12 +360,9 @@ hmm
364
360
  writing merged outputs from 2 subsets to test/paired/new-results/subset-partition-new-simu/merged-subsets
365
361
  writing combined h/l info to fasta and meta files in test/paired/new-results/subset-partition-new-simu/merged-subsets
366
362
  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
367
- tag: v1.0.11
368
- tag: v1.0.11
369
- tag: v1.0.11
370
363
  run 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
371
364
  log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
372
- total time: 68.2
365
+ total time: 68.1
373
366
  seed-partition-new-simu 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
374
367
  removing seqs very different from seed seq
375
368
  wrong/no removed singly kept missing
@@ -407,7 +400,7 @@ getting annotations for final partition
407
400
  reading output
408
401
  read 12 hmm output lines with 17 sequences in 12 events (0 failures)
409
402
  hmm step time: 0.3
410
- total time: 1.9
403
+ total time: 2.0
411
404
  partition igk:
412
405
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
413
406
  run 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
@@ -430,7 +423,7 @@ hmm
430
423
  getting annotations for final partition
431
424
  subcluster annotating 2 clusters with steps: (0.1s) (0.1s) (0.1s)
432
425
  subcluster annotation time 0.2
433
- total time: 0.7
426
+ total time: 0.6
434
427
  partition igl:
435
428
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
436
429
  run partis partition --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --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-igl.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -492,7 +485,6 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
492
485
  merge time 0.0
493
486
  removed 7 unseeded clusters (of 8 total, leaving 1) from igh joint partition
494
487
  seed cluster size in best joint partition: 1, excluding seed seq: 0
495
- tag: v1.0.11
496
488
  annotate igh+igk: igh
497
489
  removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
498
490
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -514,7 +506,6 @@ hmm
514
506
  removed 7 unseeded clusters (of 8 total, leaving 1) from igk joint partition
515
507
  need to get annotations for 1/1 joint igk clusters
516
508
  seed cluster size in best joint partition: 1, excluding seed seq: 0
517
- tag: v1.0.11
518
509
  annotate igh+igk: igk
519
510
  removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
520
511
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -561,7 +552,7 @@ hmm
561
552
  N clusters with all seqs:
562
553
  h 12 --> 1 -11
563
554
  k 2 --> 1 -1
564
- total time: 9.3
555
+ total time: 9.4
565
556
  get-selection-metrics-new-simu 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
566
557
  get-selection-metrics igh+igk: igh
567
558
  run 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
@@ -685,7 +676,7 @@ hmm
685
676
  total time: 5.6
686
677
  cache-parameters-data 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
687
678
  note: --paired-outdir is not set, so there will be no persistent record of the results (except the parameter directory).
688
- run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/275115/meta.yaml --n-max-queries 100
679
+ run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/749815/meta.yaml --n-max-queries 100
689
680
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
690
681
  extract_pairing_info(): read 100 sequences with 48 droplet ids
691
682
  droplet id separators (set automatically): _ indices: [0]
@@ -696,9 +687,9 @@ hmm
696
687
  2 42 0.875
697
688
  3 2 0.042
698
689
  4 2 0.042
699
- run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/275115 --input-metafname /tmp/runner/hmms/275115/meta.yaml --n-max-queries 100
690
+ run 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
700
691
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
701
- --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/275115/meta.yaml: paired-uids
692
+ --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
702
693
  read pairing info for 100 seqs from input meta file
703
694
  running vsearch on 100 sequences:
704
695
  igh: 49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
@@ -721,10 +712,10 @@ totals: igh 48 igk 37 igl 15
721
712
  2 0.13 h l
722
713
  1 0.07 h k
723
714
  1 0.07 h h k
724
- writing to /tmp/runner/hmms/275115/
725
- igh: 48 to 275115/igh.fa
726
- igk: 37 to 275115/igk.fa
727
- igl: 15 to 275115/igl.fa
715
+ writing to /tmp/runner/hmms/749815/
716
+ igh: 48 to 749815/igh.fa
717
+ igk: 37 to 749815/igk.fa
718
+ igl: 15 to 749815/igl.fa
728
719
  writing to paired subdirs
729
720
  igh+igk:
730
721
  igh: 36 / 48 to igh+igk/igh.fa
@@ -733,8 +724,8 @@ writing to paired subdirs
733
724
  igh: 15 / 48 to igh+igl/igh.fa
734
725
  igl: 15 / 15 to igh+igl/igl.fa
735
726
  cache-parameters igh:
736
- run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/275115/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/275115/meta.yaml
737
- --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/275115/meta.yaml: paired-uids
727
+ run 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
728
+ --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
738
729
  caching parameters
739
730
  vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.0 sec
740
731
  keeping 23 / 198 v genes
@@ -753,7 +744,7 @@ smith-waterman (writing parameters)
753
744
  writing parameters to test/paired/new-results/test/parameters/data/igh/sw (2.0 sec)
754
745
  water time: 2.2 (ig-sw 2.1 processing 0.1)
755
746
  writing hmms removed 13 genes from glfo (leaving v 23 d 19 j 6)
756
- (1.0 sec)
747
+ (0.9 sec)
757
748
  hmm
758
749
  reading output
759
750
  read 48 hmm output lines with 48 sequences in 48 events (0 failures)
@@ -761,11 +752,11 @@ hmm
761
752
  infra time: 2.0
762
753
  hmm step time: 3.0
763
754
  writing hmms removed 1 genes from glfo (leaving v 23 d 18 j 6)
764
- (1.0 sec)
755
+ (0.9 sec)
765
756
  total time: 7.5
766
757
  cache-parameters igk:
767
- run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/275115/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/275115/meta.yaml
768
- --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/275115/meta.yaml: paired-uids
758
+ run 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
759
+ --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
769
760
  caching parameters
770
761
  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.0 sec
771
762
  keeping 16 / 64 v genes
@@ -781,7 +772,7 @@ smith-waterman (writing parameters)
781
772
  info for 37 / 37 = 1.000 (removed: 0 failed)
782
773
  kept 1 (0.027) unproductive
783
774
  writing sw results to test/paired/new-results/test/parameters/data/igk/sw-cache.yaml
784
- writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.3 sec)
775
+ writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.4 sec)
785
776
  water time: 1.5 (ig-sw 1.4 processing 0.1)
786
777
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
787
778
  (1.0 sec)
@@ -789,14 +780,14 @@ hmm
789
780
  reading output
790
781
  read 37 hmm output lines with 37 sequences in 37 events (0 failures)
791
782
  writing parameters to test/paired/new-results/test/parameters/data/igk/hmm (1.3 sec)
792
- infra time: 1.3
783
+ infra time: 1.4
793
784
  hmm step time: 1.9
794
785
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
795
786
  (1.0 sec)
796
787
  total time: 5.7
797
788
  cache-parameters igl:
798
- run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/275115/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/275115/meta.yaml
799
- --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/275115/meta.yaml: paired-uids
789
+ run 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
790
+ --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
800
791
  caching parameters
801
792
  vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.0 sec
802
793
  keeping 10 / 80 v genes
@@ -823,5 +814,5 @@ hmm
823
814
  writing hmms removed 0 genes from glfo (leaving v 10 d 1 j 3)
824
815
  (0.6 sec)
825
816
  total time: 3.5
826
- warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/275115/: failed.fa
817
+ warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/749815/: failed.fa
827
818
  total time: 21.8