partis-bcr 1.0.5__py3-none-any.whl → 1.0.6__py3-none-any.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 (137) hide show
  1. bin/partis-test.py +4 -1
  2. packages/ham/bcrham +0 -0
  3. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/partis-test.py +4 -1
  4. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/METADATA +1 -1
  5. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/RECORD +97 -137
  6. test/new-results/test/parameters/simu/hmm/all-mean-mute-freqs.csv +3 -3
  7. test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv +11 -11
  8. test/new-results/test/parameters/simu/hmm/all-probs.csv +3 -13
  9. test/new-results/test/parameters/simu/hmm/cluster_size.csv +1 -1
  10. test/new-results/test/parameters/simu/hmm/d-mean-mute-freqs.csv +6 -6
  11. test/new-results/test/parameters/simu/hmm/d-mean-n-muted.csv +3 -3
  12. test/new-results/test/parameters/simu/hmm/d_gene-d_3p_del-probs.csv +1 -6
  13. test/new-results/test/parameters/simu/hmm/d_gene-d_5p_del-probs.csv +2 -9
  14. test/new-results/test/parameters/simu/hmm/d_gene-probs.csv +1 -5
  15. test/new-results/test/parameters/simu/hmm/d_gene-vd_insertion-probs.csv +2 -10
  16. test/new-results/test/parameters/simu/hmm/dj_insertion_content.csv +4 -4
  17. test/new-results/test/parameters/simu/hmm/fv_insertion-probs.csv +2 -3
  18. test/new-results/test/parameters/simu/hmm/germline-sets/igh/extras.csv +0 -6
  19. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighd.fasta +0 -8
  20. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighj.fasta +0 -2
  21. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighv.fasta +0 -10
  22. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-13_star_01.yaml +268 -267
  23. test/new-results/test/parameters/simu/hmm/hmms/IGHJ4_star_02.yaml +306 -306
  24. test/new-results/test/parameters/simu/hmm/hmms/IGHJ6_star_02.yaml +284 -284
  25. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-66_star_02.yaml +1191 -1191
  26. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-7_star_05.yaml +2 -2
  27. test/new-results/test/parameters/simu/hmm/j-mean-mute-freqs.csv +5 -5
  28. test/new-results/test/parameters/simu/hmm/j-mean-n-muted.csv +4 -4
  29. test/new-results/test/parameters/simu/hmm/j_gene-dj_insertion-probs.csv +2 -9
  30. test/new-results/test/parameters/simu/hmm/j_gene-j_3p_del-probs.csv +1 -2
  31. test/new-results/test/parameters/simu/hmm/j_gene-j_5p_del-probs.csv +2 -7
  32. test/new-results/test/parameters/simu/hmm/j_gene-probs.csv +1 -2
  33. test/new-results/test/parameters/simu/hmm/jf_insertion-probs.csv +1 -1
  34. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-13_star_01.csv +13 -16
  35. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ4_star_02.csv +40 -44
  36. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ6_star_02.csv +0 -2
  37. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-66_star_02.csv +291 -293
  38. test/new-results/test/parameters/simu/hmm/seq_content.csv +4 -4
  39. test/new-results/test/parameters/simu/hmm/v-mean-mute-freqs.csv +3 -3
  40. test/new-results/test/parameters/simu/hmm/v-mean-n-muted.csv +7 -7
  41. test/new-results/test/parameters/simu/hmm/v_gene-probs.csv +1 -6
  42. test/new-results/test/parameters/simu/hmm/v_gene-v_3p_del-probs.csv +1 -7
  43. test/new-results/test/parameters/simu/hmm/v_gene-v_5p_del-probs.csv +1 -6
  44. test/new-results/test/parameters/simu/hmm/vd_insertion_content.csv +4 -4
  45. test/new-results/test/parameters/simu/sw/all-mean-mute-freqs.csv +3 -3
  46. test/new-results/test/parameters/simu/sw/all-mean-n-muted.csv +8 -8
  47. test/new-results/test/parameters/simu/sw/all-probs.csv +1 -9
  48. test/new-results/test/parameters/simu/sw/cluster_size.csv +1 -1
  49. test/new-results/test/parameters/simu/sw/d-mean-mute-freqs.csv +5 -5
  50. test/new-results/test/parameters/simu/sw/d-mean-n-muted.csv +3 -3
  51. test/new-results/test/parameters/simu/sw/d_gene-d_3p_del-probs.csv +1 -7
  52. test/new-results/test/parameters/simu/sw/d_gene-d_5p_del-probs.csv +1 -7
  53. test/new-results/test/parameters/simu/sw/d_gene-probs.csv +1 -5
  54. test/new-results/test/parameters/simu/sw/d_gene-vd_insertion-probs.csv +1 -8
  55. test/new-results/test/parameters/simu/sw/dj_insertion_content.csv +4 -4
  56. test/new-results/test/parameters/simu/sw/fv_insertion-probs.csv +1 -1
  57. test/new-results/test/parameters/simu/sw/germline-sets/igh/extras.csv +0 -6
  58. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighd.fasta +0 -8
  59. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighj.fasta +0 -2
  60. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighv.fasta +0 -10
  61. test/new-results/test/parameters/simu/sw/hmms/IGHD6-13_star_01.yaml +268 -267
  62. test/new-results/test/parameters/simu/sw/hmms/IGHJ4_star_02.yaml +306 -306
  63. test/new-results/test/parameters/simu/sw/hmms/IGHJ6_star_02.yaml +22 -22
  64. test/new-results/test/parameters/simu/sw/hmms/IGHV3-66_star_02.yaml +1191 -1191
  65. test/new-results/test/parameters/simu/sw/hmms/IGHV3-7_star_05.yaml +2 -2
  66. test/new-results/test/parameters/simu/sw/j-mean-mute-freqs.csv +4 -4
  67. test/new-results/test/parameters/simu/sw/j-mean-n-muted.csv +3 -3
  68. test/new-results/test/parameters/simu/sw/j_gene-dj_insertion-probs.csv +1 -7
  69. test/new-results/test/parameters/simu/sw/j_gene-j_3p_del-probs.csv +1 -2
  70. test/new-results/test/parameters/simu/sw/j_gene-j_5p_del-probs.csv +1 -7
  71. test/new-results/test/parameters/simu/sw/j_gene-probs.csv +1 -2
  72. test/new-results/test/parameters/simu/sw/jf_insertion-probs.csv +1 -1
  73. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-13_star_01.csv +13 -16
  74. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ4_star_02.csv +40 -48
  75. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv +291 -293
  76. test/new-results/test/parameters/simu/sw/seq_content.csv +4 -4
  77. test/new-results/test/parameters/simu/sw/v-mean-mute-freqs.csv +3 -3
  78. test/new-results/test/parameters/simu/sw/v-mean-n-muted.csv +7 -7
  79. test/new-results/test/parameters/simu/sw/v_gene-probs.csv +1 -6
  80. test/new-results/test/parameters/simu/sw/v_gene-v_3p_del-probs.csv +1 -7
  81. test/new-results/test/parameters/simu/sw/v_gene-v_5p_del-probs.csv +1 -6
  82. test/new-results/test/parameters/simu/sw/vd_insertion_content.csv +4 -4
  83. test/new-results/test/parameters/simu/sw-cache.yaml +1 -1
  84. test/new-results/test.log +24 -258
  85. test/test.py +4 -1
  86. test/new-results/test/parameters/simu/hmm/hmms/IGHD1-20_star_01.yaml +0 -449
  87. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-16_star_02.yaml +0 -870
  88. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-22_star_01.yaml +0 -744
  89. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-19_star_01.yaml +0 -534
  90. test/new-results/test/parameters/simu/hmm/hmms/IGHJ1_star_01.yaml +0 -986
  91. test/new-results/test/parameters/simu/hmm/hmms/IGHV1-18_star_01.yaml +0 -4484
  92. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-23_star_01.yaml +0 -4484
  93. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-4_star_09.yaml +0 -4438
  94. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-61_star_01.yaml +0 -4529
  95. test/new-results/test/parameters/simu/hmm/hmms/IGHV5-51_star_01.yaml +0 -4484
  96. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD1-20_star_01.csv +0 -9
  97. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-16_star_02.csv +0 -30
  98. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-22_star_01.csv +0 -32
  99. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-19_star_01.csv +0 -22
  100. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ1_star_01.csv +0 -50
  101. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV1-18_star_01.csv +0 -297
  102. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-23_star_01.csv +0 -297
  103. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-4_star_09.csv +0 -291
  104. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-61_star_01.csv +0 -300
  105. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV5-51_star_01.csv +0 -296
  106. test/new-results/test/parameters/simu/sw/hmms/IGHD1-20_star_01.yaml +0 -449
  107. test/new-results/test/parameters/simu/sw/hmms/IGHD3-16_star_02.yaml +0 -870
  108. test/new-results/test/parameters/simu/sw/hmms/IGHD3-22_star_01.yaml +0 -744
  109. test/new-results/test/parameters/simu/sw/hmms/IGHD6-19_star_01.yaml +0 -534
  110. test/new-results/test/parameters/simu/sw/hmms/IGHJ1_star_01.yaml +0 -986
  111. test/new-results/test/parameters/simu/sw/hmms/IGHV1-18_star_01.yaml +0 -4484
  112. test/new-results/test/parameters/simu/sw/hmms/IGHV3-23_star_01.yaml +0 -4484
  113. test/new-results/test/parameters/simu/sw/hmms/IGHV4-4_star_09.yaml +0 -4438
  114. test/new-results/test/parameters/simu/sw/hmms/IGHV4-61_star_01.yaml +0 -4529
  115. test/new-results/test/parameters/simu/sw/hmms/IGHV5-51_star_01.yaml +0 -4484
  116. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD1-20_star_01.csv +0 -9
  117. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-16_star_02.csv +0 -30
  118. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-22_star_01.csv +0 -32
  119. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-19_star_01.csv +0 -20
  120. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ1_star_01.csv +0 -50
  121. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV1-18_star_01.csv +0 -297
  122. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-23_star_01.csv +0 -297
  123. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-4_star_09.csv +0 -291
  124. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-61_star_01.csv +0 -300
  125. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV5-51_star_01.csv +0 -296
  126. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/cf-alleles.py +0 -0
  127. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/cf-germlines.py +0 -0
  128. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/compare-plotdirs.py +0 -0
  129. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/extract-pairing-info.py +0 -0
  130. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/gctree-run.py +0 -0
  131. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/get-naive-probabilities.py +0 -0
  132. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/parse-output.py +0 -0
  133. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/split-loci.py +0 -0
  134. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/WHEEL +0 -0
  135. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/entry_points.txt +0 -0
  136. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/licenses/COPYING +0 -0
  137. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/hmm/hmms/IGHJ1_star_01.yaml DELETED
@@ -1,986 +0,0 @@
1
- !!python/object:python.hmmwriter.HMM
2
- extras:
3
- gene_prob: 0.2222222222222222
4
- overall_mute_freq: 0.012499999999999999
5
- per_gene_mute_freq: 0.10705817872396202
6
- name: IGHJ1_star_01
7
- states:
8
- - !!python/object:python.hmmwriter.State
9
- emissions: null
10
- extras: {}
11
- name: init
12
- transitions:
13
- IGHJ1_star_01_0: 0.007954545454545452
14
- IGHJ1_star_01_1: 0.007954545454545452
15
- IGHJ1_star_01_10: 0.002651515151515152
16
- IGHJ1_star_01_11: 0.0013257575757575767
17
- IGHJ1_star_01_12: 1.3246979271095615e-18
18
- IGHJ1_star_01_13: 0.007954545454545452
19
- IGHJ1_star_01_14: 0.007954545454545452
20
- IGHJ1_star_01_15: 0.007954545454545452
21
- IGHJ1_star_01_16: 0.007954545454545452
22
- IGHJ1_star_01_17: 0.007954545454545452
23
- IGHJ1_star_01_18: 0.007954545454545452
24
- IGHJ1_star_01_2: 0.007954545454545452
25
- IGHJ1_star_01_3: 0.05568181818181816
26
- IGHJ1_star_01_4: 0.039772727272727265
27
- IGHJ1_star_01_5: 0.023863636363636358
28
- IGHJ1_star_01_6: 0.007954545454545452
29
- IGHJ1_star_01_7: 0.006628787878787877
30
- IGHJ1_star_01_8: 0.0053030303030303025
31
- IGHJ1_star_01_9: 0.003977272727272727
32
- insert_left_A: 0.09486607142857142
33
- insert_left_C: 0.31808035714285715
34
- insert_left_G: 0.12276785714285714
35
- insert_left_T: 0.24553571428571427
36
- - !!python/object:python.hmmwriter.State
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- emissions:
38
- probs:
39
- A: 0.8929418212760379
40
- C: 0.035686059574654004
41
- G: 0.035686059574654004
42
- T: 0.035686059574654004
43
- track: nukes
44
- extras:
45
- ambiguous_char: N
46
- ambiguous_emission_prob: 0.25
47
- germline: A
48
- name: insert_left_A
49
- transitions:
50
- IGHJ1_star_01_0: 0.015311004784688994
51
- IGHJ1_star_01_1: 0.015311004784688994
52
- IGHJ1_star_01_10: 0.005103668261563
53
- IGHJ1_star_01_11: 0.0025518341307815017
54
- IGHJ1_star_01_12: 2.5497945063161486e-18
55
- IGHJ1_star_01_13: 0.015311004784688994
56
- IGHJ1_star_01_14: 0.015311004784688994
57
- IGHJ1_star_01_15: 0.015311004784688994
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- IGHJ1_star_01_16: 0.015311004784688994
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- IGHJ1_star_01_17: 0.015311004784688994
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- IGHJ1_star_01_18: 0.015311004784688994
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- IGHJ1_star_01_2: 0.015311004784688994
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- IGHJ1_star_01_3: 0.10717703349282295
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- IGHJ1_star_01_4: 0.07655502392344497
64
- IGHJ1_star_01_5: 0.04593301435406698
65
- IGHJ1_star_01_6: 0.015311004784688994
66
- IGHJ1_star_01_7: 0.012759170653907496
67
- IGHJ1_star_01_8: 0.010207336523125998
68
- IGHJ1_star_01_9: 0.007655502392344499
69
- insert_left_A: 0.07030075187969925
70
- insert_left_C: 0.2357142857142857
71
- insert_left_G: 0.09097744360902256
72
- insert_left_T: 0.18195488721804512
73
- - !!python/object:python.hmmwriter.State
74
- emissions:
75
- probs:
76
- A: 0.035686059574654004
77
- C: 0.8929418212760379
78
- G: 0.035686059574654004
79
- T: 0.035686059574654004
80
- track: nukes
81
- extras:
82
- ambiguous_char: N
83
- ambiguous_emission_prob: 0.25
84
- germline: C
85
- name: insert_left_C
86
- transitions:
87
- IGHJ1_star_01_0: 0.015311004784688994
88
- IGHJ1_star_01_1: 0.015311004784688994
89
- IGHJ1_star_01_10: 0.005103668261563
90
- IGHJ1_star_01_11: 0.0025518341307815017
91
- IGHJ1_star_01_12: 2.5497945063161486e-18
92
- IGHJ1_star_01_13: 0.015311004784688994
93
- IGHJ1_star_01_14: 0.015311004784688994
94
- IGHJ1_star_01_15: 0.015311004784688994
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- IGHJ1_star_01_16: 0.015311004784688994
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- IGHJ1_star_01_17: 0.015311004784688994
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- IGHJ1_star_01_18: 0.015311004784688994
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- IGHJ1_star_01_2: 0.015311004784688994
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- IGHJ1_star_01_3: 0.10717703349282295
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- IGHJ1_star_01_4: 0.07655502392344497
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- IGHJ1_star_01_5: 0.04593301435406698
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- IGHJ1_star_01_6: 0.015311004784688994
103
- IGHJ1_star_01_7: 0.012759170653907496
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- IGHJ1_star_01_8: 0.010207336523125998
105
- IGHJ1_star_01_9: 0.007655502392344499
106
- insert_left_A: 0.07030075187969925
107
- insert_left_C: 0.2357142857142857
108
- insert_left_G: 0.09097744360902256
109
- insert_left_T: 0.18195488721804512
110
- - !!python/object:python.hmmwriter.State
111
- emissions:
112
- probs:
113
- A: 0.035686059574654004
114
- C: 0.035686059574654004
115
- G: 0.8929418212760379
116
- T: 0.035686059574654004
117
- track: nukes
118
- extras:
119
- ambiguous_char: N
120
- ambiguous_emission_prob: 0.25
121
- germline: G
122
- name: insert_left_G
123
- transitions:
124
- IGHJ1_star_01_0: 0.015311004784688994
125
- IGHJ1_star_01_1: 0.015311004784688994
126
- IGHJ1_star_01_10: 0.005103668261563
127
- IGHJ1_star_01_11: 0.0025518341307815017
128
- IGHJ1_star_01_12: 2.5497945063161486e-18
129
- IGHJ1_star_01_13: 0.015311004784688994
130
- IGHJ1_star_01_14: 0.015311004784688994
131
- IGHJ1_star_01_15: 0.015311004784688994
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- IGHJ1_star_01_16: 0.015311004784688994
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- IGHJ1_star_01_17: 0.015311004784688994
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- IGHJ1_star_01_18: 0.015311004784688994
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- IGHJ1_star_01_2: 0.015311004784688994
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- IGHJ1_star_01_3: 0.10717703349282295
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- IGHJ1_star_01_4: 0.07655502392344497
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- IGHJ1_star_01_5: 0.04593301435406698
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- IGHJ1_star_01_6: 0.015311004784688994
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- IGHJ1_star_01_7: 0.012759170653907496
141
- IGHJ1_star_01_8: 0.010207336523125998
142
- IGHJ1_star_01_9: 0.007655502392344499
143
- insert_left_A: 0.07030075187969925
144
- insert_left_C: 0.2357142857142857
145
- insert_left_G: 0.09097744360902256
146
- insert_left_T: 0.18195488721804512
147
- - !!python/object:python.hmmwriter.State
148
- emissions:
149
- probs:
150
- A: 0.035686059574654004
151
- C: 0.035686059574654004
152
- G: 0.035686059574654004
153
- T: 0.8929418212760379
154
- track: nukes
155
- extras:
156
- ambiguous_char: N
157
- ambiguous_emission_prob: 0.25
158
- germline: T
159
- name: insert_left_T
160
- transitions:
161
- IGHJ1_star_01_0: 0.015311004784688994
162
- IGHJ1_star_01_1: 0.015311004784688994
163
- IGHJ1_star_01_10: 0.005103668261563
164
- IGHJ1_star_01_11: 0.0025518341307815017
165
- IGHJ1_star_01_12: 2.5497945063161486e-18
166
- IGHJ1_star_01_13: 0.015311004784688994
167
- IGHJ1_star_01_14: 0.015311004784688994
168
- IGHJ1_star_01_15: 0.015311004784688994
169
- IGHJ1_star_01_16: 0.015311004784688994
170
- IGHJ1_star_01_17: 0.015311004784688994
171
- IGHJ1_star_01_18: 0.015311004784688994
172
- IGHJ1_star_01_2: 0.015311004784688994
173
- IGHJ1_star_01_3: 0.10717703349282295
174
- IGHJ1_star_01_4: 0.07655502392344497
175
- IGHJ1_star_01_5: 0.04593301435406698
176
- IGHJ1_star_01_6: 0.015311004784688994
177
- IGHJ1_star_01_7: 0.012759170653907496
178
- IGHJ1_star_01_8: 0.010207336523125998
179
- IGHJ1_star_01_9: 0.007655502392344499
180
- insert_left_A: 0.07030075187969925
181
- insert_left_C: 0.2357142857142857
182
- insert_left_G: 0.09097744360902256
183
- insert_left_T: 0.18195488721804512
184
- - !!python/object:python.hmmwriter.State
185
- emissions:
186
- probs:
187
- A: 0.035686059574654004
188
- C: 0.035686059574654004
189
- G: 0.8929418212760379
190
- T: 0.035686059574654004
191
- track: nukes
192
- extras:
193
- ambiguous_char: N
194
- ambiguous_emission_prob: 0.25
195
- germline: G
196
- name: IGHJ1_star_01_0
197
- transitions:
198
- IGHJ1_star_01_1: 1.0
199
- - !!python/object:python.hmmwriter.State
200
- emissions:
201
- probs:
202
- A: 0.03556842326258797
203
- C: 0.893294730212236
204
- G: 0.03556842326258797
205
- T: 0.03556842326258797
206
- track: nukes
207
- extras:
208
- ambiguous_char: N
209
- ambiguous_emission_prob: 0.25
210
- germline: C
211
- name: IGHJ1_star_01_1
212
- transitions:
213
- IGHJ1_star_01_2: 1.0
214
- - !!python/object:python.hmmwriter.State
215
- emissions:
216
- probs:
217
- A: 0.03545078695052194
218
- C: 0.03545078695052194
219
- G: 0.03545078695052194
220
- T: 0.8936476391484341
221
- track: nukes
222
- extras:
223
- ambiguous_char: N
224
- ambiguous_emission_prob: 0.25
225
- germline: T
226
- name: IGHJ1_star_01_2
227
- transitions:
228
- IGHJ1_star_01_3: 1.0
229
- - !!python/object:python.hmmwriter.State
230
- emissions:
231
- probs:
232
- A: 0.03584550287504965
233
- C: 0.03584550287504965
234
- G: 0.892463491374851
235
- T: 0.03584550287504965
236
- track: nukes
237
- extras:
238
- ambiguous_char: N
239
- ambiguous_emission_prob: 0.25
240
- germline: G
241
- name: IGHJ1_star_01_3
242
- transitions:
243
- IGHJ1_star_01_4: 1.0
244
- - !!python/object:python.hmmwriter.State
245
- emissions:
246
- probs:
247
- A: 0.8923040480744554
248
- C: 0.035898650641848204
249
- G: 0.035898650641848204
250
- T: 0.035898650641848204
251
- track: nukes
252
- extras:
253
- ambiguous_char: N
254
- ambiguous_emission_prob: 0.25
255
- germline: A
256
- name: IGHJ1_star_01_4
257
- transitions:
258
- IGHJ1_star_01_5: 1.0
259
- - !!python/object:python.hmmwriter.State
260
- emissions:
261
- probs:
262
- A: 0.8921446047740598
263
- C: 0.035951798408646755
264
- G: 0.035951798408646755
265
- T: 0.035951798408646755
266
- track: nukes
267
- extras:
268
- ambiguous_char: N
269
- ambiguous_emission_prob: 0.25
270
- germline: A
271
- name: IGHJ1_star_01_5
272
- transitions:
273
- IGHJ1_star_01_6: 1.0
274
- - !!python/object:python.hmmwriter.State
275
- emissions:
276
- probs:
277
- A: 0.035980241702257804
278
- C: 0.035980241702257804
279
- G: 0.035980241702257804
280
- T: 0.8920592748932266
281
- track: nukes
282
- extras:
283
- ambiguous_char: N
284
- ambiguous_emission_prob: 0.25
285
- germline: T
286
- name: IGHJ1_star_01_6
287
- transitions:
288
- IGHJ1_star_01_7: 1.0
289
- - !!python/object:python.hmmwriter.State
290
- emissions:
291
- probs:
292
- A: 0.8919121838294247
293
- C: 0.036029272056858436
294
- G: 0.036029272056858436
295
- T: 0.036029272056858436
296
- track: nukes
297
- extras:
298
- ambiguous_char: N
299
- ambiguous_emission_prob: 0.25
300
- germline: A
301
- name: IGHJ1_star_01_7
302
- transitions:
303
- IGHJ1_star_01_8: 1.0
304
- - !!python/object:python.hmmwriter.State
305
- emissions:
306
- probs:
307
- A: 0.03607830241145907
308
- C: 0.8917650927656228
309
- G: 0.03607830241145907
310
- T: 0.03607830241145907
311
- track: nukes
312
- extras:
313
- ambiguous_char: N
314
- ambiguous_emission_prob: 0.25
315
- germline: C
316
- name: IGHJ1_star_01_8
317
- transitions:
318
- IGHJ1_star_01_9: 1.0
319
- - !!python/object:python.hmmwriter.State
320
- emissions:
321
- probs:
322
- A: 0.0356747138372197
323
- C: 0.0356747138372197
324
- G: 0.0356747138372197
325
- T: 0.8929758584883409
326
- track: nukes
327
- extras:
328
- ambiguous_char: N
329
- ambiguous_emission_prob: 0.25
330
- germline: T
331
- name: IGHJ1_star_01_9
332
- transitions:
333
- IGHJ1_star_01_10: 1.0
334
- - !!python/object:python.hmmwriter.State
335
- emissions:
336
- probs:
337
- A: 0.03567345319972701
338
- C: 0.03567345319972701
339
- G: 0.03567345319972701
340
- T: 0.892979640400819
341
- track: nukes
342
- extras:
343
- ambiguous_char: N
344
- ambiguous_emission_prob: 0.25
345
- germline: T
346
- name: IGHJ1_star_01_10
347
- transitions:
348
- IGHJ1_star_01_11: 1.0
349
- - !!python/object:python.hmmwriter.State
350
- emissions:
351
- probs:
352
- A: 0.035672192562234306
353
- C: 0.8929834223132971
354
- G: 0.035672192562234306
355
- T: 0.035672192562234306
356
- track: nukes
357
- extras:
358
- ambiguous_char: N
359
- ambiguous_emission_prob: 0.25
360
- germline: C
361
- name: IGHJ1_star_01_11
362
- transitions:
363
- IGHJ1_star_01_12: 1.0
364
- - !!python/object:python.hmmwriter.State
365
- emissions:
366
- probs:
367
- A: 0.0356709319247416
368
- C: 0.8929872042257752
369
- G: 0.0356709319247416
370
- T: 0.0356709319247416
371
- track: nukes
372
- extras:
373
- ambiguous_char: N
374
- ambiguous_emission_prob: 0.25
375
- germline: C
376
- name: IGHJ1_star_01_12
377
- transitions:
378
- IGHJ1_star_01_13: 1.0
379
- - !!python/object:python.hmmwriter.State
380
- emissions:
381
- probs:
382
- A: 0.8929909861382533
383
- C: 0.0356696712872489
384
- G: 0.0356696712872489
385
- T: 0.0356696712872489
386
- track: nukes
387
- extras:
388
- ambiguous_char: N
389
- ambiguous_emission_prob: 0.25
390
- germline: A
391
- name: IGHJ1_star_01_13
392
- transitions:
393
- IGHJ1_star_01_14: 1.0
394
- - !!python/object:python.hmmwriter.State
395
- emissions:
396
- probs:
397
- A: 0.035668410649756205
398
- C: 0.035668410649756205
399
- G: 0.8929947680507314
400
- T: 0.035668410649756205
401
- track: nukes
402
- extras:
403
- ambiguous_char: N
404
- ambiguous_emission_prob: 0.25
405
- germline: G
406
- name: IGHJ1_star_01_14
407
- transitions:
408
- IGHJ1_star_01_15: 1.0
409
- - !!python/object:python.hmmwriter.State
410
- emissions:
411
- probs:
412
- A: 0.035667150012263504
413
- C: 0.8929985499632095
414
- G: 0.035667150012263504
415
- T: 0.035667150012263504
416
- track: nukes
417
- extras:
418
- ambiguous_char: N
419
- ambiguous_emission_prob: 0.25
420
- germline: C
421
- name: IGHJ1_star_01_15
422
- transitions:
423
- IGHJ1_star_01_16: 1.0
424
- - !!python/object:python.hmmwriter.State
425
- emissions:
426
- probs:
427
- A: 0.8930023318756876
428
- C: 0.035665889374770804
429
- G: 0.035665889374770804
430
- T: 0.035665889374770804
431
- track: nukes
432
- extras:
433
- ambiguous_char: N
434
- ambiguous_emission_prob: 0.25
435
- germline: A
436
- name: IGHJ1_star_01_16
437
- transitions:
438
- IGHJ1_star_01_17: 1.0
439
- - !!python/object:python.hmmwriter.State
440
- emissions:
441
- probs:
442
- A: 0.035664628737278097
443
- C: 0.8930061137881657
444
- G: 0.035664628737278097
445
- T: 0.035664628737278097
446
- track: nukes
447
- extras:
448
- ambiguous_char: N
449
- ambiguous_emission_prob: 0.25
450
- germline: C
451
- name: IGHJ1_star_01_17
452
- transitions:
453
- IGHJ1_star_01_18: 1.0
454
- - !!python/object:python.hmmwriter.State
455
- emissions:
456
- probs:
457
- A: 0.0356633680997854
458
- C: 0.0356633680997854
459
- G: 0.0356633680997854
460
- T: 0.8930098957006438
461
- track: nukes
462
- extras:
463
- ambiguous_char: N
464
- ambiguous_emission_prob: 0.25
465
- germline: T
466
- name: IGHJ1_star_01_18
467
- transitions:
468
- IGHJ1_star_01_19: 1.0
469
- - !!python/object:python.hmmwriter.State
470
- emissions:
471
- probs:
472
- A: 0.0356621074622927
473
- C: 0.0356621074622927
474
- G: 0.8930136776131219
475
- T: 0.0356621074622927
476
- track: nukes
477
- extras:
478
- ambiguous_char: N
479
- ambiguous_emission_prob: 0.25
480
- germline: G
481
- name: IGHJ1_star_01_19
482
- transitions:
483
- IGHJ1_star_01_20: 1.0
484
- - !!python/object:python.hmmwriter.State
485
- emissions:
486
- probs:
487
- A: 0.0356608468248
488
- C: 0.0356608468248
489
- G: 0.8930174595256
490
- T: 0.0356608468248
491
- track: nukes
492
- extras:
493
- ambiguous_char: N
494
- ambiguous_emission_prob: 0.25
495
- germline: G
496
- name: IGHJ1_star_01_20
497
- transitions:
498
- IGHJ1_star_01_21: 1.0
499
- - !!python/object:python.hmmwriter.State
500
- emissions:
501
- probs:
502
- A: 0.03666666666666667
503
- C: 0.03666666666666667
504
- G: 0.89
505
- T: 0.03666666666666667
506
- track: nukes
507
- extras:
508
- ambiguous_char: N
509
- ambiguous_emission_prob: 0.25
510
- germline: G
511
- name: IGHJ1_star_01_21
512
- transitions:
513
- IGHJ1_star_01_22: 1.0
514
- - !!python/object:python.hmmwriter.State
515
- emissions:
516
- probs:
517
- A: 0.0356608468248
518
- C: 0.0356608468248
519
- G: 0.8930174595256
520
- T: 0.0356608468248
521
- track: nukes
522
- extras:
523
- ambiguous_char: N
524
- ambiguous_emission_prob: 0.25
525
- germline: G
526
- name: IGHJ1_star_01_22
527
- transitions:
528
- IGHJ1_star_01_23: 1.0
529
- - !!python/object:python.hmmwriter.State
530
- emissions:
531
- probs:
532
- A: 0.0356608468248
533
- C: 0.8930174595256
534
- G: 0.0356608468248
535
- T: 0.0356608468248
536
- track: nukes
537
- extras:
538
- ambiguous_char: N
539
- ambiguous_emission_prob: 0.25
540
- germline: C
541
- name: IGHJ1_star_01_23
542
- transitions:
543
- IGHJ1_star_01_24: 1.0
544
- - !!python/object:python.hmmwriter.State
545
- emissions:
546
- probs:
547
- A: 0.0356608468248
548
- C: 0.8930174595256
549
- G: 0.0356608468248
550
- T: 0.0356608468248
551
- track: nukes
552
- extras:
553
- ambiguous_char: N
554
- ambiguous_emission_prob: 0.25
555
- germline: C
556
- name: IGHJ1_star_01_24
557
- transitions:
558
- IGHJ1_star_01_25: 1.0
559
- - !!python/object:python.hmmwriter.State
560
- emissions:
561
- probs:
562
- A: 0.8930174595256
563
- C: 0.0356608468248
564
- G: 0.0356608468248
565
- T: 0.0356608468248
566
- track: nukes
567
- extras:
568
- ambiguous_char: N
569
- ambiguous_emission_prob: 0.25
570
- germline: A
571
- name: IGHJ1_star_01_25
572
- transitions:
573
- IGHJ1_star_01_26: 1.0
574
- - !!python/object:python.hmmwriter.State
575
- emissions:
576
- probs:
577
- A: 0.0356608468248
578
- C: 0.0356608468248
579
- G: 0.8930174595256
580
- T: 0.0356608468248
581
- track: nukes
582
- extras:
583
- ambiguous_char: N
584
- ambiguous_emission_prob: 0.25
585
- germline: G
586
- name: IGHJ1_star_01_26
587
- transitions:
588
- IGHJ1_star_01_27: 1.0
589
- - !!python/object:python.hmmwriter.State
590
- emissions:
591
- probs:
592
- A: 0.0356608468248
593
- C: 0.0356608468248
594
- G: 0.8930174595256
595
- T: 0.0356608468248
596
- track: nukes
597
- extras:
598
- ambiguous_char: N
599
- ambiguous_emission_prob: 0.25
600
- germline: G
601
- name: IGHJ1_star_01_27
602
- transitions:
603
- IGHJ1_star_01_28: 1.0
604
- - !!python/object:python.hmmwriter.State
605
- emissions:
606
- probs:
607
- A: 0.0356608468248
608
- C: 0.0356608468248
609
- G: 0.8930174595256
610
- T: 0.0356608468248
611
- track: nukes
612
- extras:
613
- ambiguous_char: N
614
- ambiguous_emission_prob: 0.25
615
- germline: G
616
- name: IGHJ1_star_01_28
617
- transitions:
618
- IGHJ1_star_01_29: 1.0
619
- - !!python/object:python.hmmwriter.State
620
- emissions:
621
- probs:
622
- A: 0.0356608468248
623
- C: 0.8930174595256
624
- G: 0.0356608468248
625
- T: 0.0356608468248
626
- track: nukes
627
- extras:
628
- ambiguous_char: N
629
- ambiguous_emission_prob: 0.25
630
- germline: C
631
- name: IGHJ1_star_01_29
632
- transitions:
633
- IGHJ1_star_01_30: 1.0
634
- - !!python/object:python.hmmwriter.State
635
- emissions:
636
- probs:
637
- A: 0.8930174595256
638
- C: 0.0356608468248
639
- G: 0.0356608468248
640
- T: 0.0356608468248
641
- track: nukes
642
- extras:
643
- ambiguous_char: N
644
- ambiguous_emission_prob: 0.25
645
- germline: A
646
- name: IGHJ1_star_01_30
647
- transitions:
648
- IGHJ1_star_01_31: 1.0
649
- - !!python/object:python.hmmwriter.State
650
- emissions:
651
- probs:
652
- A: 0.03666666666666667
653
- C: 0.89
654
- G: 0.03666666666666667
655
- T: 0.03666666666666667
656
- track: nukes
657
- extras:
658
- ambiguous_char: N
659
- ambiguous_emission_prob: 0.25
660
- germline: C
661
- name: IGHJ1_star_01_31
662
- transitions:
663
- IGHJ1_star_01_32: 1.0
664
- - !!python/object:python.hmmwriter.State
665
- emissions:
666
- probs:
667
- A: 0.0356608468248
668
- C: 0.8930174595256
669
- G: 0.0356608468248
670
- T: 0.0356608468248
671
- track: nukes
672
- extras:
673
- ambiguous_char: N
674
- ambiguous_emission_prob: 0.25
675
- germline: C
676
- name: IGHJ1_star_01_32
677
- transitions:
678
- IGHJ1_star_01_33: 1.0
679
- - !!python/object:python.hmmwriter.State
680
- emissions:
681
- probs:
682
- A: 0.0356608468248
683
- C: 0.8930174595256
684
- G: 0.0356608468248
685
- T: 0.0356608468248
686
- track: nukes
687
- extras:
688
- ambiguous_char: N
689
- ambiguous_emission_prob: 0.25
690
- germline: C
691
- name: IGHJ1_star_01_33
692
- transitions:
693
- IGHJ1_star_01_34: 1.0
694
- - !!python/object:python.hmmwriter.State
695
- emissions:
696
- probs:
697
- A: 0.0356608468248
698
- C: 0.0356608468248
699
- G: 0.0356608468248
700
- T: 0.8930174595256
701
- track: nukes
702
- extras:
703
- ambiguous_char: N
704
- ambiguous_emission_prob: 0.25
705
- germline: T
706
- name: IGHJ1_star_01_34
707
- transitions:
708
- IGHJ1_star_01_35: 1.0
709
- - !!python/object:python.hmmwriter.State
710
- emissions:
711
- probs:
712
- A: 0.0356608468248
713
- C: 0.0356608468248
714
- G: 0.8930174595256
715
- T: 0.0356608468248
716
- track: nukes
717
- extras:
718
- ambiguous_char: N
719
- ambiguous_emission_prob: 0.25
720
- germline: G
721
- name: IGHJ1_star_01_35
722
- transitions:
723
- IGHJ1_star_01_36: 1.0
724
- - !!python/object:python.hmmwriter.State
725
- emissions:
726
- probs:
727
- A: 0.0356608468248
728
- C: 0.0356608468248
729
- G: 0.8930174595256
730
- T: 0.0356608468248
731
- track: nukes
732
- extras:
733
- ambiguous_char: N
734
- ambiguous_emission_prob: 0.25
735
- germline: G
736
- name: IGHJ1_star_01_36
737
- transitions:
738
- IGHJ1_star_01_37: 1.0
739
- - !!python/object:python.hmmwriter.State
740
- emissions:
741
- probs:
742
- A: 0.0356608468248
743
- C: 0.0356608468248
744
- G: 0.0356608468248
745
- T: 0.8930174595256
746
- track: nukes
747
- extras:
748
- ambiguous_char: N
749
- ambiguous_emission_prob: 0.25
750
- germline: T
751
- name: IGHJ1_star_01_37
752
- transitions:
753
- IGHJ1_star_01_38: 1.0
754
- - !!python/object:python.hmmwriter.State
755
- emissions:
756
- probs:
757
- A: 0.0356608468248
758
- C: 0.8930174595256
759
- G: 0.0356608468248
760
- T: 0.0356608468248
761
- track: nukes
762
- extras:
763
- ambiguous_char: N
764
- ambiguous_emission_prob: 0.25
765
- germline: C
766
- name: IGHJ1_star_01_38
767
- transitions:
768
- IGHJ1_star_01_39: 1.0
769
- - !!python/object:python.hmmwriter.State
770
- emissions:
771
- probs:
772
- A: 0.8930174595256
773
- C: 0.0356608468248
774
- G: 0.0356608468248
775
- T: 0.0356608468248
776
- track: nukes
777
- extras:
778
- ambiguous_char: N
779
- ambiguous_emission_prob: 0.25
780
- germline: A
781
- name: IGHJ1_star_01_39
782
- transitions:
783
- IGHJ1_star_01_40: 1.0
784
- - !!python/object:python.hmmwriter.State
785
- emissions:
786
- probs:
787
- A: 0.0356608468248
788
- C: 0.8930174595256
789
- G: 0.0356608468248
790
- T: 0.0356608468248
791
- track: nukes
792
- extras:
793
- ambiguous_char: N
794
- ambiguous_emission_prob: 0.25
795
- germline: C
796
- name: IGHJ1_star_01_40
797
- transitions:
798
- IGHJ1_star_01_41: 1.0
799
- - !!python/object:python.hmmwriter.State
800
- emissions:
801
- probs:
802
- A: 0.0356608468248
803
- C: 0.8930174595256
804
- G: 0.0356608468248
805
- T: 0.0356608468248
806
- track: nukes
807
- extras:
808
- ambiguous_char: N
809
- ambiguous_emission_prob: 0.25
810
- germline: C
811
- name: IGHJ1_star_01_41
812
- transitions:
813
- IGHJ1_star_01_42: 1.0
814
- - !!python/object:python.hmmwriter.State
815
- emissions:
816
- probs:
817
- A: 0.0356608468248
818
- C: 0.0356608468248
819
- G: 0.8930174595256
820
- T: 0.0356608468248
821
- track: nukes
822
- extras:
823
- ambiguous_char: N
824
- ambiguous_emission_prob: 0.25
825
- germline: G
826
- name: IGHJ1_star_01_42
827
- transitions:
828
- IGHJ1_star_01_43: 1.0
829
- - !!python/object:python.hmmwriter.State
830
- emissions:
831
- probs:
832
- A: 0.0356608468248
833
- C: 0.0356608468248
834
- G: 0.0356608468248
835
- T: 0.8930174595256
836
- track: nukes
837
- extras:
838
- ambiguous_char: N
839
- ambiguous_emission_prob: 0.25
840
- germline: T
841
- name: IGHJ1_star_01_43
842
- transitions:
843
- IGHJ1_star_01_44: 1.0
844
- - !!python/object:python.hmmwriter.State
845
- emissions:
846
- probs:
847
- A: 0.0356608468248
848
- C: 0.8930174595256
849
- G: 0.0356608468248
850
- T: 0.0356608468248
851
- track: nukes
852
- extras:
853
- ambiguous_char: N
854
- ambiguous_emission_prob: 0.25
855
- germline: C
856
- name: IGHJ1_star_01_44
857
- transitions:
858
- IGHJ1_star_01_45: 1.0
859
- - !!python/object:python.hmmwriter.State
860
- emissions:
861
- probs:
862
- A: 0.0356608468248
863
- C: 0.0356608468248
864
- G: 0.0356608468248
865
- T: 0.8930174595256
866
- track: nukes
867
- extras:
868
- ambiguous_char: N
869
- ambiguous_emission_prob: 0.25
870
- germline: T
871
- name: IGHJ1_star_01_45
872
- transitions:
873
- IGHJ1_star_01_46: 1.0
874
- - !!python/object:python.hmmwriter.State
875
- emissions:
876
- probs:
877
- A: 0.0356608468248
878
- C: 0.8930174595256
879
- G: 0.0356608468248
880
- T: 0.0356608468248
881
- track: nukes
882
- extras:
883
- ambiguous_char: N
884
- ambiguous_emission_prob: 0.25
885
- germline: C
886
- name: IGHJ1_star_01_46
887
- transitions:
888
- IGHJ1_star_01_47: 1.0
889
- - !!python/object:python.hmmwriter.State
890
- emissions:
891
- probs:
892
- A: 0.0356608468248
893
- C: 0.8930174595256
894
- G: 0.0356608468248
895
- T: 0.0356608468248
896
- track: nukes
897
- extras:
898
- ambiguous_char: N
899
- ambiguous_emission_prob: 0.25
900
- germline: C
901
- name: IGHJ1_star_01_47
902
- transitions:
903
- IGHJ1_star_01_48: 1.0
904
- - !!python/object:python.hmmwriter.State
905
- emissions:
906
- probs:
907
- A: 0.0356608468248
908
- C: 0.0356608468248
909
- G: 0.0356608468248
910
- T: 0.8930174595256
911
- track: nukes
912
- extras:
913
- ambiguous_char: N
914
- ambiguous_emission_prob: 0.25
915
- germline: T
916
- name: IGHJ1_star_01_48
917
- transitions:
918
- IGHJ1_star_01_49: 1.0
919
- - !!python/object:python.hmmwriter.State
920
- emissions:
921
- probs:
922
- A: 0.0356608468248
923
- C: 0.8930174595256
924
- G: 0.0356608468248
925
- T: 0.0356608468248
926
- track: nukes
927
- extras:
928
- ambiguous_char: N
929
- ambiguous_emission_prob: 0.25
930
- germline: C
931
- name: IGHJ1_star_01_49
932
- transitions:
933
- IGHJ1_star_01_50: 1.0
934
- - !!python/object:python.hmmwriter.State
935
- emissions:
936
- probs:
937
- A: 0.8930174595256
938
- C: 0.0356608468248
939
- G: 0.0356608468248
940
- T: 0.0356608468248
941
- track: nukes
942
- extras:
943
- ambiguous_char: N
944
- ambiguous_emission_prob: 0.25
945
- germline: A
946
- name: IGHJ1_star_01_50
947
- transitions:
948
- IGHJ1_star_01_51: 1.0
949
- - !!python/object:python.hmmwriter.State
950
- emissions:
951
- probs:
952
- A: 0.0356608468248
953
- C: 0.0356608468248
954
- G: 0.8930174595256
955
- T: 0.0356608468248
956
- track: nukes
957
- extras:
958
- ambiguous_char: N
959
- ambiguous_emission_prob: 0.25
960
- germline: G
961
- name: IGHJ1_star_01_51
962
- transitions:
963
- end: 0.04
964
- insert_right_N: 0.96
965
- - !!python/object:python.hmmwriter.State
966
- emissions:
967
- probs:
968
- A: 0.25
969
- C: 0.25
970
- G: 0.25
971
- T: 0.25
972
- track: nukes
973
- extras:
974
- ambiguous_char: N
975
- ambiguous_emission_prob: 0.25
976
- germline: N
977
- name: insert_right_N
978
- transitions:
979
- end: 0.040000000000000036
980
- insert_right_N: 0.96
981
- tracks:
982
- nukes:
983
- - A
984
- - C
985
- - G
986
- - T