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/sw/hmms/IGHD6-19_star_01.yaml DELETED
@@ -1,534 +0,0 @@
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- !!python/object:python.hmmwriter.HMM
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- extras:
3
- gene_prob: 0.027777777777777776
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- overall_mute_freq: 0.012222222222222223
5
- per_gene_mute_freq: 0.10689027397084408
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- name: IGHD6-19_star_01
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- states:
8
- - !!python/object:python.hmmwriter.State
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- emissions: null
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- extras: {}
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- name: init
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- transitions:
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- IGHD6-19_star_01_0: 0.023809523809523808
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- IGHD6-19_star_01_1: 0.023809523809523808
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- IGHD6-19_star_01_10: 0.023809523809523808
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- IGHD6-19_star_01_11: 0.023809523809523808
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- IGHD6-19_star_01_12: 0.023809523809523808
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- IGHD6-19_star_01_13: 0.023809523809523808
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- IGHD6-19_star_01_14: 0.023809523809523808
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- IGHD6-19_star_01_15: 0.023809523809523808
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- IGHD6-19_star_01_16: 0.023809523809523808
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- IGHD6-19_star_01_17: 0.023809523809523808
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- IGHD6-19_star_01_18: 0.023809523809523808
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- IGHD6-19_star_01_19: 0.023809523809523808
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- IGHD6-19_star_01_2: 0.023809523809523808
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- IGHD6-19_star_01_20: 0.023809523809523808
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- IGHD6-19_star_01_3: 0.023809523809523808
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- IGHD6-19_star_01_4: 0.023809523809523808
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- IGHD6-19_star_01_5: 0.023809523809523808
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- IGHD6-19_star_01_6: 0.023809523809523808
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- IGHD6-19_star_01_7: 0.023809523809523808
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- IGHD6-19_star_01_8: 0.023809523809523808
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- IGHD6-19_star_01_9: 0.023809523809523808
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- insert_left_A: 0.06206896551724138
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- insert_left_C: 0.2206896551724138
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- insert_left_G: 0.08620689655172414
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- insert_left_T: 0.1310344827586207
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- - !!python/object:python.hmmwriter.State
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- emissions:
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- probs:
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- A: 0.893109726029156
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- C: 0.03563009132361469
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- G: 0.03563009132361469
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- T: 0.03563009132361469
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- track: nukes
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- extras:
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- ambiguous_char: N
48
- ambiguous_emission_prob: 0.25
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- germline: A
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- name: insert_left_A
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- transitions:
52
- IGHD6-19_star_01_0: 0.023809523809523808
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- IGHD6-19_star_01_1: 0.023809523809523808
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- IGHD6-19_star_01_10: 0.023809523809523808
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- IGHD6-19_star_01_11: 0.023809523809523808
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- IGHD6-19_star_01_12: 0.023809523809523808
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- IGHD6-19_star_01_13: 0.023809523809523808
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- IGHD6-19_star_01_14: 0.023809523809523808
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- IGHD6-19_star_01_15: 0.023809523809523808
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- IGHD6-19_star_01_16: 0.023809523809523808
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- IGHD6-19_star_01_17: 0.023809523809523808
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- IGHD6-19_star_01_18: 0.023809523809523808
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- IGHD6-19_star_01_19: 0.023809523809523808
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- IGHD6-19_star_01_2: 0.023809523809523808
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- IGHD6-19_star_01_20: 0.023809523809523808
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- IGHD6-19_star_01_3: 0.023809523809523808
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- IGHD6-19_star_01_4: 0.023809523809523808
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- IGHD6-19_star_01_5: 0.023809523809523808
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- IGHD6-19_star_01_6: 0.023809523809523808
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- IGHD6-19_star_01_7: 0.023809523809523808
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- IGHD6-19_star_01_8: 0.023809523809523808
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- IGHD6-19_star_01_9: 0.023809523809523808
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- insert_left_A: 0.06206896551724138
74
- insert_left_C: 0.2206896551724138
75
- insert_left_G: 0.08620689655172414
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- insert_left_T: 0.1310344827586207
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- - !!python/object:python.hmmwriter.State
78
- emissions:
79
- probs:
80
- A: 0.03563009132361469
81
- C: 0.893109726029156
82
- G: 0.03563009132361469
83
- T: 0.03563009132361469
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- track: nukes
85
- extras:
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- ambiguous_char: N
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- ambiguous_emission_prob: 0.25
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- germline: C
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- name: insert_left_C
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- transitions:
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- IGHD6-19_star_01_0: 0.023809523809523808
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- IGHD6-19_star_01_1: 0.023809523809523808
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- IGHD6-19_star_01_10: 0.023809523809523808
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- IGHD6-19_star_01_11: 0.023809523809523808
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- IGHD6-19_star_01_12: 0.023809523809523808
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- IGHD6-19_star_01_13: 0.023809523809523808
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- IGHD6-19_star_01_14: 0.023809523809523808
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- IGHD6-19_star_01_15: 0.023809523809523808
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- IGHD6-19_star_01_16: 0.023809523809523808
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- IGHD6-19_star_01_17: 0.023809523809523808
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- IGHD6-19_star_01_18: 0.023809523809523808
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- IGHD6-19_star_01_19: 0.023809523809523808
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- IGHD6-19_star_01_2: 0.023809523809523808
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- IGHD6-19_star_01_20: 0.023809523809523808
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- IGHD6-19_star_01_3: 0.023809523809523808
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- IGHD6-19_star_01_4: 0.023809523809523808
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- IGHD6-19_star_01_5: 0.023809523809523808
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- IGHD6-19_star_01_6: 0.023809523809523808
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- IGHD6-19_star_01_7: 0.023809523809523808
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- IGHD6-19_star_01_8: 0.023809523809523808
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- IGHD6-19_star_01_9: 0.023809523809523808
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- insert_left_A: 0.06206896551724138
113
- insert_left_C: 0.2206896551724138
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- insert_left_G: 0.08620689655172414
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- insert_left_T: 0.1310344827586207
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- - !!python/object:python.hmmwriter.State
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- emissions:
118
- probs:
119
- A: 0.03563009132361469
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- C: 0.03563009132361469
121
- G: 0.893109726029156
122
- T: 0.03563009132361469
123
- track: nukes
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- extras:
125
- ambiguous_char: N
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- ambiguous_emission_prob: 0.25
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- germline: G
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- name: insert_left_G
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- transitions:
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- IGHD6-19_star_01_0: 0.023809523809523808
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- IGHD6-19_star_01_1: 0.023809523809523808
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- IGHD6-19_star_01_10: 0.023809523809523808
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- IGHD6-19_star_01_11: 0.023809523809523808
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- IGHD6-19_star_01_12: 0.023809523809523808
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- IGHD6-19_star_01_13: 0.023809523809523808
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- IGHD6-19_star_01_14: 0.023809523809523808
137
- IGHD6-19_star_01_15: 0.023809523809523808
138
- IGHD6-19_star_01_16: 0.023809523809523808
139
- IGHD6-19_star_01_17: 0.023809523809523808
140
- IGHD6-19_star_01_18: 0.023809523809523808
141
- IGHD6-19_star_01_19: 0.023809523809523808
142
- IGHD6-19_star_01_2: 0.023809523809523808
143
- IGHD6-19_star_01_20: 0.023809523809523808
144
- IGHD6-19_star_01_3: 0.023809523809523808
145
- IGHD6-19_star_01_4: 0.023809523809523808
146
- IGHD6-19_star_01_5: 0.023809523809523808
147
- IGHD6-19_star_01_6: 0.023809523809523808
148
- IGHD6-19_star_01_7: 0.023809523809523808
149
- IGHD6-19_star_01_8: 0.023809523809523808
150
- IGHD6-19_star_01_9: 0.023809523809523808
151
- insert_left_A: 0.06206896551724138
152
- insert_left_C: 0.2206896551724138
153
- insert_left_G: 0.08620689655172414
154
- insert_left_T: 0.1310344827586207
155
- - !!python/object:python.hmmwriter.State
156
- emissions:
157
- probs:
158
- A: 0.03563009132361469
159
- C: 0.03563009132361469
160
- G: 0.03563009132361469
161
- T: 0.893109726029156
162
- track: nukes
163
- extras:
164
- ambiguous_char: N
165
- ambiguous_emission_prob: 0.25
166
- germline: T
167
- name: insert_left_T
168
- transitions:
169
- IGHD6-19_star_01_0: 0.023809523809523808
170
- IGHD6-19_star_01_1: 0.023809523809523808
171
- IGHD6-19_star_01_10: 0.023809523809523808
172
- IGHD6-19_star_01_11: 0.023809523809523808
173
- IGHD6-19_star_01_12: 0.023809523809523808
174
- IGHD6-19_star_01_13: 0.023809523809523808
175
- IGHD6-19_star_01_14: 0.023809523809523808
176
- IGHD6-19_star_01_15: 0.023809523809523808
177
- IGHD6-19_star_01_16: 0.023809523809523808
178
- IGHD6-19_star_01_17: 0.023809523809523808
179
- IGHD6-19_star_01_18: 0.023809523809523808
180
- IGHD6-19_star_01_19: 0.023809523809523808
181
- IGHD6-19_star_01_2: 0.023809523809523808
182
- IGHD6-19_star_01_20: 0.023809523809523808
183
- IGHD6-19_star_01_3: 0.023809523809523808
184
- IGHD6-19_star_01_4: 0.023809523809523808
185
- IGHD6-19_star_01_5: 0.023809523809523808
186
- IGHD6-19_star_01_6: 0.023809523809523808
187
- IGHD6-19_star_01_7: 0.023809523809523808
188
- IGHD6-19_star_01_8: 0.023809523809523808
189
- IGHD6-19_star_01_9: 0.023809523809523808
190
- insert_left_A: 0.06206896551724138
191
- insert_left_C: 0.2206896551724138
192
- insert_left_G: 0.08620689655172414
193
- insert_left_T: 0.1310344827586207
194
- - !!python/object:python.hmmwriter.State
195
- emissions:
196
- probs:
197
- A: 0.03563009132361469
198
- C: 0.03563009132361469
199
- G: 0.893109726029156
200
- T: 0.03563009132361469
201
- track: nukes
202
- extras:
203
- ambiguous_char: N
204
- ambiguous_emission_prob: 0.25
205
- germline: G
206
- name: IGHD6-19_star_01_0
207
- transitions:
208
- IGHD6-19_star_01_1: 0.9512195121951219
209
- end: 0.04878048780487805
210
- - !!python/object:python.hmmwriter.State
211
- emissions:
212
- probs:
213
- A: 0.03565695399016769
214
- C: 0.03565695399016769
215
- G: 0.8930291380294969
216
- T: 0.03565695399016769
217
- track: nukes
218
- extras:
219
- ambiguous_char: N
220
- ambiguous_emission_prob: 0.25
221
- germline: G
222
- name: IGHD6-19_star_01_1
223
- transitions:
224
- IGHD6-19_star_01_2: 0.9512195121951219
225
- end: 0.04878048780487805
226
- - !!python/object:python.hmmwriter.State
227
- emissions:
228
- probs:
229
- A: 0.03568381665672069
230
- C: 0.03568381665672069
231
- G: 0.892948550029838
232
- T: 0.03568381665672069
233
- track: nukes
234
- extras:
235
- ambiguous_char: N
236
- ambiguous_emission_prob: 0.25
237
- germline: G
238
- name: IGHD6-19_star_01_2
239
- transitions:
240
- IGHD6-19_star_01_3: 0.9512195121951219
241
- end: 0.04878048780487805
242
- - !!python/object:python.hmmwriter.State
243
- emissions:
244
- probs:
245
- A: 0.03571067932327369
246
- C: 0.03571067932327369
247
- G: 0.03571067932327369
248
- T: 0.8928679620301789
249
- track: nukes
250
- extras:
251
- ambiguous_char: N
252
- ambiguous_emission_prob: 0.25
253
- germline: T
254
- name: IGHD6-19_star_01_3
255
- transitions:
256
- IGHD6-19_star_01_4: 0.9512195121951219
257
- end: 0.04878048780487805
258
- - !!python/object:python.hmmwriter.State
259
- emissions:
260
- probs:
261
- A: 0.8927873740305199
262
- C: 0.035737541989826684
263
- G: 0.035737541989826684
264
- T: 0.035737541989826684
265
- track: nukes
266
- extras:
267
- ambiguous_char: N
268
- ambiguous_emission_prob: 0.25
269
- germline: A
270
- name: IGHD6-19_star_01_4
271
- transitions:
272
- IGHD6-19_star_01_5: 0.9512195121951219
273
- end: 0.04878048780487805
274
- - !!python/object:python.hmmwriter.State
275
- emissions:
276
- probs:
277
- A: 0.03576440465637968
278
- C: 0.03576440465637968
279
- G: 0.03576440465637968
280
- T: 0.892706786030861
281
- track: nukes
282
- extras:
283
- ambiguous_char: N
284
- ambiguous_emission_prob: 0.25
285
- germline: T
286
- name: IGHD6-19_star_01_5
287
- transitions:
288
- IGHD6-19_star_01_6: 0.9512195121951219
289
- end: 0.04878048780487805
290
- - !!python/object:python.hmmwriter.State
291
- emissions:
292
- probs:
293
- A: 0.8926261980312019
294
- C: 0.03579126732293268
295
- G: 0.03579126732293268
296
- T: 0.03579126732293268
297
- track: nukes
298
- extras:
299
- ambiguous_char: N
300
- ambiguous_emission_prob: 0.25
301
- germline: A
302
- name: IGHD6-19_star_01_6
303
- transitions:
304
- IGHD6-19_star_01_7: 0.9512195121951219
305
- end: 0.04878048780487805
306
- - !!python/object:python.hmmwriter.State
307
- emissions:
308
- probs:
309
- A: 0.03581812998948568
310
- C: 0.03581812998948568
311
- G: 0.892545610031543
312
- T: 0.03581812998948568
313
- track: nukes
314
- extras:
315
- ambiguous_char: N
316
- ambiguous_emission_prob: 0.25
317
- germline: G
318
- name: IGHD6-19_star_01_7
319
- transitions:
320
- IGHD6-19_star_01_8: 0.9512195121951219
321
- end: 0.04878048780487805
322
- - !!python/object:python.hmmwriter.State
323
- emissions:
324
- probs:
325
- A: 0.035844992656038674
326
- C: 0.8924650220318839
327
- G: 0.035844992656038674
328
- T: 0.035844992656038674
329
- track: nukes
330
- extras:
331
- ambiguous_char: N
332
- ambiguous_emission_prob: 0.25
333
- germline: C
334
- name: IGHD6-19_star_01_8
335
- transitions:
336
- IGHD6-19_star_01_9: 0.9512195121951219
337
- end: 0.04878048780487805
338
- - !!python/object:python.hmmwriter.State
339
- emissions:
340
- probs:
341
- A: 0.892384434032225
342
- C: 0.03587185532259167
343
- G: 0.03587185532259167
344
- T: 0.03587185532259167
345
- track: nukes
346
- extras:
347
- ambiguous_char: N
348
- ambiguous_emission_prob: 0.25
349
- germline: A
350
- name: IGHD6-19_star_01_9
351
- transitions:
352
- IGHD6-19_star_01_10: 0.9512195121951219
353
- end: 0.04878048780487805
354
- - !!python/object:python.hmmwriter.State
355
- emissions:
356
- probs:
357
- A: 0.03587185532259167
358
- C: 0.03587185532259167
359
- G: 0.892384434032225
360
- T: 0.03587185532259167
361
- track: nukes
362
- extras:
363
- ambiguous_char: N
364
- ambiguous_emission_prob: 0.25
365
- germline: G
366
- name: IGHD6-19_star_01_10
367
- transitions:
368
- IGHD6-19_star_01_11: 0.9512195121951219
369
- end: 0.04878048780487805
370
- - !!python/object:python.hmmwriter.State
371
- emissions:
372
- probs:
373
- A: 0.03587185532259167
374
- C: 0.03587185532259167
375
- G: 0.03587185532259167
376
- T: 0.892384434032225
377
- track: nukes
378
- extras:
379
- ambiguous_char: N
380
- ambiguous_emission_prob: 0.25
381
- germline: T
382
- name: IGHD6-19_star_01_11
383
- transitions:
384
- IGHD6-19_star_01_12: 0.9512195121951219
385
- end: 0.04878048780487805
386
- - !!python/object:python.hmmwriter.State
387
- emissions:
388
- probs:
389
- A: 0.035844992656038674
390
- C: 0.035844992656038674
391
- G: 0.8924650220318839
392
- T: 0.035844992656038674
393
- track: nukes
394
- extras:
395
- ambiguous_char: N
396
- ambiguous_emission_prob: 0.25
397
- germline: G
398
- name: IGHD6-19_star_01_12
399
- transitions:
400
- IGHD6-19_star_01_13: 0.9512195121951219
401
- end: 0.04878048780487805
402
- - !!python/object:python.hmmwriter.State
403
- emissions:
404
- probs:
405
- A: 0.03581812998948568
406
- C: 0.03581812998948568
407
- G: 0.892545610031543
408
- T: 0.03581812998948568
409
- track: nukes
410
- extras:
411
- ambiguous_char: N
412
- ambiguous_emission_prob: 0.25
413
- germline: G
414
- name: IGHD6-19_star_01_13
415
- transitions:
416
- IGHD6-19_star_01_14: 0.9512195121951219
417
- end: 0.04878048780487805
418
- - !!python/object:python.hmmwriter.State
419
- emissions:
420
- probs:
421
- A: 0.03579126732293268
422
- C: 0.8926261980312019
423
- G: 0.03579126732293268
424
- T: 0.03579126732293268
425
- track: nukes
426
- extras:
427
- ambiguous_char: N
428
- ambiguous_emission_prob: 0.25
429
- germline: C
430
- name: IGHD6-19_star_01_14
431
- transitions:
432
- IGHD6-19_star_01_15: 0.9512195121951219
433
- end: 0.04878048780487805
434
- - !!python/object:python.hmmwriter.State
435
- emissions:
436
- probs:
437
- A: 0.03576440465637968
438
- C: 0.03576440465637968
439
- G: 0.03576440465637968
440
- T: 0.892706786030861
441
- track: nukes
442
- extras:
443
- ambiguous_char: N
444
- ambiguous_emission_prob: 0.25
445
- germline: T
446
- name: IGHD6-19_star_01_15
447
- transitions:
448
- IGHD6-19_star_01_16: 0.9512195121951219
449
- end: 0.04878048780487805
450
- - !!python/object:python.hmmwriter.State
451
- emissions:
452
- probs:
453
- A: 0.035737541989826684
454
- C: 0.035737541989826684
455
- G: 0.8927873740305199
456
- T: 0.035737541989826684
457
- track: nukes
458
- extras:
459
- ambiguous_char: N
460
- ambiguous_emission_prob: 0.25
461
- germline: G
462
- name: IGHD6-19_star_01_16
463
- transitions:
464
- IGHD6-19_star_01_17: 0.9512195121951219
465
- end: 0.04878048780487805
466
- - !!python/object:python.hmmwriter.State
467
- emissions:
468
- probs:
469
- A: 0.03571067932327369
470
- C: 0.03571067932327369
471
- G: 0.8928679620301789
472
- T: 0.03571067932327369
473
- track: nukes
474
- extras:
475
- ambiguous_char: N
476
- ambiguous_emission_prob: 0.25
477
- germline: G
478
- name: IGHD6-19_star_01_17
479
- transitions:
480
- IGHD6-19_star_01_18: 0.975609756097561
481
- end: 0.024390243902439025
482
- - !!python/object:python.hmmwriter.State
483
- emissions:
484
- probs:
485
- A: 0.03568381665672069
486
- C: 0.03568381665672069
487
- G: 0.03568381665672069
488
- T: 0.892948550029838
489
- track: nukes
490
- extras:
491
- ambiguous_char: N
492
- ambiguous_emission_prob: 0.25
493
- germline: T
494
- name: IGHD6-19_star_01_18
495
- transitions:
496
- IGHD6-19_star_01_19: 0.9512195121951219
497
- end: 0.04878048780487805
498
- - !!python/object:python.hmmwriter.State
499
- emissions:
500
- probs:
501
- A: 0.8938753120259164
502
- C: 0.035374895991361205
503
- G: 0.035374895991361205
504
- T: 0.035374895991361205
505
- track: nukes
506
- extras:
507
- ambiguous_char: N
508
- ambiguous_emission_prob: 0.25
509
- germline: A
510
- name: IGHD6-19_star_01_19
511
- transitions:
512
- IGHD6-19_star_01_20: 0.9512195121951219
513
- end: 0.04878048780487805
514
- - !!python/object:python.hmmwriter.State
515
- emissions:
516
- probs:
517
- A: 0.03563009132361469
518
- C: 0.893109726029156
519
- G: 0.03563009132361469
520
- T: 0.03563009132361469
521
- track: nukes
522
- extras:
523
- ambiguous_char: N
524
- ambiguous_emission_prob: 0.25
525
- germline: C
526
- name: IGHD6-19_star_01_20
527
- transitions:
528
- end: 1.0
529
- tracks:
530
- nukes:
531
- - A
532
- - C
533
- - G
534
- - T