partis-bcr 1.0.5__py3-none-any.whl → 1.0.7__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 (139) hide show
  1. bin/partis-test.py +4 -1
  2. packages/ham/bcrham +0 -0
  3. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/partis-test.py +4 -1
  4. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/METADATA +2 -1
  5. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/RECORD +98 -139
  6. python/utils.py +1 -1
  7. test/new-results/test/parameters/simu/hmm/all-mean-mute-freqs.csv +3 -3
  8. test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv +11 -11
  9. test/new-results/test/parameters/simu/hmm/all-probs.csv +3 -13
  10. test/new-results/test/parameters/simu/hmm/cluster_size.csv +1 -1
  11. test/new-results/test/parameters/simu/hmm/d-mean-mute-freqs.csv +6 -6
  12. test/new-results/test/parameters/simu/hmm/d-mean-n-muted.csv +3 -3
  13. test/new-results/test/parameters/simu/hmm/d_gene-d_3p_del-probs.csv +1 -6
  14. test/new-results/test/parameters/simu/hmm/d_gene-d_5p_del-probs.csv +2 -9
  15. test/new-results/test/parameters/simu/hmm/d_gene-probs.csv +1 -5
  16. test/new-results/test/parameters/simu/hmm/d_gene-vd_insertion-probs.csv +2 -10
  17. test/new-results/test/parameters/simu/hmm/dj_insertion_content.csv +4 -4
  18. test/new-results/test/parameters/simu/hmm/fv_insertion-probs.csv +2 -3
  19. test/new-results/test/parameters/simu/hmm/germline-sets/igh/extras.csv +0 -6
  20. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighd.fasta +0 -8
  21. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighj.fasta +0 -2
  22. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighv.fasta +0 -10
  23. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-13_star_01.yaml +268 -267
  24. test/new-results/test/parameters/simu/hmm/hmms/IGHJ4_star_02.yaml +306 -306
  25. test/new-results/test/parameters/simu/hmm/hmms/IGHJ6_star_02.yaml +284 -284
  26. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-66_star_02.yaml +1191 -1191
  27. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-7_star_05.yaml +2 -2
  28. test/new-results/test/parameters/simu/hmm/j-mean-mute-freqs.csv +5 -5
  29. test/new-results/test/parameters/simu/hmm/j-mean-n-muted.csv +4 -4
  30. test/new-results/test/parameters/simu/hmm/j_gene-dj_insertion-probs.csv +2 -9
  31. test/new-results/test/parameters/simu/hmm/j_gene-j_3p_del-probs.csv +1 -2
  32. test/new-results/test/parameters/simu/hmm/j_gene-j_5p_del-probs.csv +2 -7
  33. test/new-results/test/parameters/simu/hmm/j_gene-probs.csv +1 -2
  34. test/new-results/test/parameters/simu/hmm/jf_insertion-probs.csv +1 -1
  35. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-13_star_01.csv +13 -16
  36. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ4_star_02.csv +40 -44
  37. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ6_star_02.csv +0 -2
  38. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-66_star_02.csv +291 -293
  39. test/new-results/test/parameters/simu/hmm/seq_content.csv +4 -4
  40. test/new-results/test/parameters/simu/hmm/v-mean-mute-freqs.csv +3 -3
  41. test/new-results/test/parameters/simu/hmm/v-mean-n-muted.csv +7 -7
  42. test/new-results/test/parameters/simu/hmm/v_gene-probs.csv +1 -6
  43. test/new-results/test/parameters/simu/hmm/v_gene-v_3p_del-probs.csv +1 -7
  44. test/new-results/test/parameters/simu/hmm/v_gene-v_5p_del-probs.csv +1 -6
  45. test/new-results/test/parameters/simu/hmm/vd_insertion_content.csv +4 -4
  46. test/new-results/test/parameters/simu/sw/all-mean-mute-freqs.csv +3 -3
  47. test/new-results/test/parameters/simu/sw/all-mean-n-muted.csv +8 -8
  48. test/new-results/test/parameters/simu/sw/all-probs.csv +1 -9
  49. test/new-results/test/parameters/simu/sw/cluster_size.csv +1 -1
  50. test/new-results/test/parameters/simu/sw/d-mean-mute-freqs.csv +5 -5
  51. test/new-results/test/parameters/simu/sw/d-mean-n-muted.csv +3 -3
  52. test/new-results/test/parameters/simu/sw/d_gene-d_3p_del-probs.csv +1 -7
  53. test/new-results/test/parameters/simu/sw/d_gene-d_5p_del-probs.csv +1 -7
  54. test/new-results/test/parameters/simu/sw/d_gene-probs.csv +1 -5
  55. test/new-results/test/parameters/simu/sw/d_gene-vd_insertion-probs.csv +1 -8
  56. test/new-results/test/parameters/simu/sw/dj_insertion_content.csv +4 -4
  57. test/new-results/test/parameters/simu/sw/fv_insertion-probs.csv +1 -1
  58. test/new-results/test/parameters/simu/sw/germline-sets/igh/extras.csv +0 -6
  59. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighd.fasta +0 -8
  60. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighj.fasta +0 -2
  61. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighv.fasta +0 -10
  62. test/new-results/test/parameters/simu/sw/hmms/IGHD6-13_star_01.yaml +268 -267
  63. test/new-results/test/parameters/simu/sw/hmms/IGHJ4_star_02.yaml +306 -306
  64. test/new-results/test/parameters/simu/sw/hmms/IGHJ6_star_02.yaml +22 -22
  65. test/new-results/test/parameters/simu/sw/hmms/IGHV3-66_star_02.yaml +1191 -1191
  66. test/new-results/test/parameters/simu/sw/hmms/IGHV3-7_star_05.yaml +2 -2
  67. test/new-results/test/parameters/simu/sw/j-mean-mute-freqs.csv +4 -4
  68. test/new-results/test/parameters/simu/sw/j-mean-n-muted.csv +3 -3
  69. test/new-results/test/parameters/simu/sw/j_gene-dj_insertion-probs.csv +1 -7
  70. test/new-results/test/parameters/simu/sw/j_gene-j_3p_del-probs.csv +1 -2
  71. test/new-results/test/parameters/simu/sw/j_gene-j_5p_del-probs.csv +1 -7
  72. test/new-results/test/parameters/simu/sw/j_gene-probs.csv +1 -2
  73. test/new-results/test/parameters/simu/sw/jf_insertion-probs.csv +1 -1
  74. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-13_star_01.csv +13 -16
  75. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ4_star_02.csv +40 -48
  76. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv +291 -293
  77. test/new-results/test/parameters/simu/sw/seq_content.csv +4 -4
  78. test/new-results/test/parameters/simu/sw/v-mean-mute-freqs.csv +3 -3
  79. test/new-results/test/parameters/simu/sw/v-mean-n-muted.csv +7 -7
  80. test/new-results/test/parameters/simu/sw/v_gene-probs.csv +1 -6
  81. test/new-results/test/parameters/simu/sw/v_gene-v_3p_del-probs.csv +1 -7
  82. test/new-results/test/parameters/simu/sw/v_gene-v_5p_del-probs.csv +1 -6
  83. test/new-results/test/parameters/simu/sw/vd_insertion_content.csv +4 -4
  84. test/new-results/test/parameters/simu/sw-cache.yaml +1 -1
  85. test/new-results/test.log +24 -258
  86. test/test.py +4 -1
  87. bin/partis-pip +0 -116
  88. test/new-results/test/parameters/simu/hmm/hmms/IGHD1-20_star_01.yaml +0 -449
  89. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-16_star_02.yaml +0 -870
  90. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-22_star_01.yaml +0 -744
  91. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-19_star_01.yaml +0 -534
  92. test/new-results/test/parameters/simu/hmm/hmms/IGHJ1_star_01.yaml +0 -986
  93. test/new-results/test/parameters/simu/hmm/hmms/IGHV1-18_star_01.yaml +0 -4484
  94. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-23_star_01.yaml +0 -4484
  95. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-4_star_09.yaml +0 -4438
  96. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-61_star_01.yaml +0 -4529
  97. test/new-results/test/parameters/simu/hmm/hmms/IGHV5-51_star_01.yaml +0 -4484
  98. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD1-20_star_01.csv +0 -9
  99. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-16_star_02.csv +0 -30
  100. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-22_star_01.csv +0 -32
  101. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-19_star_01.csv +0 -22
  102. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ1_star_01.csv +0 -50
  103. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV1-18_star_01.csv +0 -297
  104. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-23_star_01.csv +0 -297
  105. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-4_star_09.csv +0 -291
  106. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-61_star_01.csv +0 -300
  107. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV5-51_star_01.csv +0 -296
  108. test/new-results/test/parameters/simu/sw/hmms/IGHD1-20_star_01.yaml +0 -449
  109. test/new-results/test/parameters/simu/sw/hmms/IGHD3-16_star_02.yaml +0 -870
  110. test/new-results/test/parameters/simu/sw/hmms/IGHD3-22_star_01.yaml +0 -744
  111. test/new-results/test/parameters/simu/sw/hmms/IGHD6-19_star_01.yaml +0 -534
  112. test/new-results/test/parameters/simu/sw/hmms/IGHJ1_star_01.yaml +0 -986
  113. test/new-results/test/parameters/simu/sw/hmms/IGHV1-18_star_01.yaml +0 -4484
  114. test/new-results/test/parameters/simu/sw/hmms/IGHV3-23_star_01.yaml +0 -4484
  115. test/new-results/test/parameters/simu/sw/hmms/IGHV4-4_star_09.yaml +0 -4438
  116. test/new-results/test/parameters/simu/sw/hmms/IGHV4-61_star_01.yaml +0 -4529
  117. test/new-results/test/parameters/simu/sw/hmms/IGHV5-51_star_01.yaml +0 -4484
  118. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD1-20_star_01.csv +0 -9
  119. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-16_star_02.csv +0 -30
  120. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-22_star_01.csv +0 -32
  121. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-19_star_01.csv +0 -20
  122. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ1_star_01.csv +0 -50
  123. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV1-18_star_01.csv +0 -297
  124. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-23_star_01.csv +0 -297
  125. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-4_star_09.csv +0 -291
  126. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-61_star_01.csv +0 -300
  127. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV5-51_star_01.csv +0 -296
  128. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/cf-alleles.py +0 -0
  129. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/cf-germlines.py +0 -0
  130. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/compare-plotdirs.py +0 -0
  131. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/extract-pairing-info.py +0 -0
  132. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/gctree-run.py +0 -0
  133. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/get-naive-probabilities.py +0 -0
  134. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/parse-output.py +0 -0
  135. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/split-loci.py +0 -0
  136. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/WHEEL +0 -0
  137. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/entry_points.txt +0 -0
  138. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/licenses/COPYING +0 -0
  139. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/hmm/hmms/IGHD6-19_star_01.yaml DELETED
@@ -1,534 +0,0 @@
1
- !!python/object:python.hmmwriter.HMM
2
- extras:
3
- gene_prob: 0.027777777777777776
4
- overall_mute_freq: 0.012499999999999999
5
- per_gene_mute_freq: 0.10761556596777501
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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: 0.05673758865248227
35
- insert_left_C: 0.22695035460992907
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- insert_left_G: 0.08156028368794327
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- insert_left_T: 0.1347517730496454
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- - !!python/object:python.hmmwriter.State
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- emissions:
40
- probs:
41
- A: 0.892384434032225
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- C: 0.03587185532259167
43
- G: 0.03587185532259167
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- T: 0.03587185532259167
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- track: nukes
46
- extras:
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- ambiguous_char: N
48
- ambiguous_emission_prob: 0.25
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- germline: A
50
- 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: 0.05673758865248227
74
- insert_left_C: 0.22695035460992907
75
- insert_left_G: 0.08156028368794327
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- insert_left_T: 0.1347517730496454
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- - !!python/object:python.hmmwriter.State
78
- emissions:
79
- probs:
80
- A: 0.03587185532259167
81
- C: 0.892384434032225
82
- G: 0.03587185532259167
83
- T: 0.03587185532259167
84
- track: nukes
85
- extras:
86
- ambiguous_char: N
87
- ambiguous_emission_prob: 0.25
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- germline: C
89
- name: insert_left_C
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- transitions:
91
- 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: 0.05673758865248227
113
- insert_left_C: 0.22695035460992907
114
- insert_left_G: 0.08156028368794327
115
- insert_left_T: 0.1347517730496454
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- - !!python/object:python.hmmwriter.State
117
- emissions:
118
- probs:
119
- A: 0.03587185532259167
120
- C: 0.03587185532259167
121
- G: 0.892384434032225
122
- T: 0.03587185532259167
123
- track: nukes
124
- extras:
125
- ambiguous_char: N
126
- 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
136
- 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: 0.05673758865248227
152
- insert_left_C: 0.22695035460992907
153
- insert_left_G: 0.08156028368794327
154
- insert_left_T: 0.1347517730496454
155
- - !!python/object:python.hmmwriter.State
156
- emissions:
157
- probs:
158
- A: 0.03587185532259167
159
- C: 0.03587185532259167
160
- G: 0.03587185532259167
161
- T: 0.892384434032225
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: 0.05673758865248227
191
- insert_left_C: 0.22695035460992907
192
- insert_left_G: 0.08156028368794327
193
- insert_left_T: 0.1347517730496454
194
- - !!python/object:python.hmmwriter.State
195
- emissions:
196
- probs:
197
- A: 0.03587185532259167
198
- C: 0.03587185532259167
199
- G: 0.892384434032225
200
- T: 0.03587185532259167
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: 0.9523809523809523
209
- end: 0.047619047619047616
210
- - !!python/object:python.hmmwriter.State
211
- emissions:
212
- probs:
213
- A: 0.03587185532259167
214
- C: 0.03587185532259167
215
- G: 0.892384434032225
216
- T: 0.03587185532259167
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: 0.9523809523809523
225
- end: 0.047619047619047616
226
- - !!python/object:python.hmmwriter.State
227
- emissions:
228
- probs:
229
- A: 0.03587185532259167
230
- C: 0.03587185532259167
231
- G: 0.892384434032225
232
- T: 0.03587185532259167
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: 0.9523809523809523
241
- end: 0.047619047619047616
242
- - !!python/object:python.hmmwriter.State
243
- emissions:
244
- probs:
245
- A: 0.03587185532259167
246
- C: 0.03587185532259167
247
- G: 0.03587185532259167
248
- T: 0.892384434032225
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: 0.9523809523809523
257
- end: 0.047619047619047616
258
- - !!python/object:python.hmmwriter.State
259
- emissions:
260
- probs:
261
- A: 0.892384434032225
262
- C: 0.03587185532259167
263
- G: 0.03587185532259167
264
- T: 0.03587185532259167
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: 0.9523809523809523
273
- end: 0.047619047619047616
274
- - !!python/object:python.hmmwriter.State
275
- emissions:
276
- probs:
277
- A: 0.03587185532259167
278
- C: 0.03587185532259167
279
- G: 0.03587185532259167
280
- T: 0.892384434032225
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: 0.9523809523809523
289
- end: 0.047619047619047616
290
- - !!python/object:python.hmmwriter.State
291
- emissions:
292
- probs:
293
- A: 0.892384434032225
294
- C: 0.03587185532259168
295
- G: 0.03587185532259168
296
- T: 0.03587185532259168
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: 0.9523809523809523
305
- end: 0.047619047619047616
306
- - !!python/object:python.hmmwriter.State
307
- emissions:
308
- probs:
309
- A: 0.03587185532259167
310
- C: 0.03587185532259167
311
- G: 0.892384434032225
312
- T: 0.03587185532259167
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: 0.9523809523809523
321
- end: 0.047619047619047616
322
- - !!python/object:python.hmmwriter.State
323
- emissions:
324
- probs:
325
- A: 0.03587185532259167
326
- C: 0.892384434032225
327
- G: 0.03587185532259167
328
- T: 0.03587185532259167
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: 0.9523809523809523
337
- end: 0.047619047619047616
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: 0.9523809523809523
353
- end: 0.047619047619047616
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: 0.9523809523809523
369
- end: 0.047619047619047616
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: 0.9523809523809523
385
- end: 0.047619047619047616
386
- - !!python/object:python.hmmwriter.State
387
- emissions:
388
- probs:
389
- A: 0.03587185532259167
390
- C: 0.03587185532259167
391
- G: 0.892384434032225
392
- T: 0.03587185532259167
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: 0.9523809523809523
401
- end: 0.047619047619047616
402
- - !!python/object:python.hmmwriter.State
403
- emissions:
404
- probs:
405
- A: 0.03587185532259167
406
- C: 0.03587185532259167
407
- G: 0.892384434032225
408
- T: 0.03587185532259167
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: 0.9523809523809523
417
- end: 0.047619047619047616
418
- - !!python/object:python.hmmwriter.State
419
- emissions:
420
- probs:
421
- A: 0.03587185532259168
422
- C: 0.892384434032225
423
- G: 0.03587185532259168
424
- T: 0.03587185532259168
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: 0.9523809523809523
433
- end: 0.047619047619047616
434
- - !!python/object:python.hmmwriter.State
435
- emissions:
436
- probs:
437
- A: 0.03587185532259167
438
- C: 0.03587185532259167
439
- G: 0.03587185532259167
440
- T: 0.892384434032225
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: 0.9523809523809523
449
- end: 0.047619047619047616
450
- - !!python/object:python.hmmwriter.State
451
- emissions:
452
- probs:
453
- A: 0.03587185532259167
454
- C: 0.03587185532259167
455
- G: 0.892384434032225
456
- T: 0.03587185532259167
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: 0.9523809523809523
465
- end: 0.047619047619047616
466
- - !!python/object:python.hmmwriter.State
467
- emissions:
468
- probs:
469
- A: 0.03587185532259167
470
- C: 0.03587185532259167
471
- G: 0.892384434032225
472
- T: 0.03587185532259167
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: 0.9523809523809523
481
- end: 0.047619047619047616
482
- - !!python/object:python.hmmwriter.State
483
- emissions:
484
- probs:
485
- A: 0.03587185532259167
486
- C: 0.03587185532259167
487
- G: 0.03587185532259167
488
- T: 0.892384434032225
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: 0.9523809523809523
497
- end: 0.047619047619047616
498
- - !!python/object:python.hmmwriter.State
499
- emissions:
500
- probs:
501
- A: 0.892384434032225
502
- C: 0.03587185532259167
503
- G: 0.03587185532259167
504
- T: 0.03587185532259167
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: 0.9523809523809523
513
- end: 0.047619047619047616
514
- - !!python/object:python.hmmwriter.State
515
- emissions:
516
- probs:
517
- A: 0.03587185532259167
518
- C: 0.892384434032225
519
- G: 0.03587185532259167
520
- T: 0.03587185532259167
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