partis-bcr 1.0.11.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl → 1.0.11.post1.dev7__cp312-cp312-macosx_10_13_universal2.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 (645) hide show
  1. bin/partis +1 -1
  2. bin/partis-test.py +6 -0
  3. bin/partis.py +1 -1
  4. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +645 -127
  7. python/recombinator.py +2 -0
  8. python/treegenerator.py +1 -1
  9. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  10. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +8 -0
  11. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  12. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  13. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  14. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  15. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  16. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  17. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  18. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  19. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +8 -0
  20. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  21. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  22. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  23. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  24. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  25. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  26. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  27. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  28. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  29. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +7 -0
  30. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +7 -0
  31. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +5 -0
  32. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +6 -0
  33. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +7 -0
  34. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  35. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  36. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  37. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +7 -0
  38. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  39. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  40. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  41. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  42. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  43. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  44. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  45. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  46. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  47. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  48. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  49. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  50. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  51. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  52. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  53. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  54. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  55. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  56. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  57. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  58. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  59. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  60. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  61. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  62. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  63. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  64. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  65. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  66. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  67. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  68. test/new-results/annotate-new-simu.yaml +1 -0
  69. test/new-results/cache-new-partition.csv +59 -0
  70. test/new-results/get-selection-metrics-new-simu.yaml +1 -0
  71. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  72. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  73. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  74. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  75. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  76. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  77. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  78. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  79. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  80. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  81. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  82. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  83. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  84. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  85. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  86. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  87. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  88. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  89. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  90. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  91. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  92. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  93. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  94. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  95. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  96. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  97. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  98. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  99. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  100. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  101. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  102. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  103. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  104. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  105. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  106. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  107. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  108. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  109. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  110. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  111. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  112. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  113. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  114. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  115. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  116. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  117. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  118. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  119. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  120. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  121. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  122. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  123. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  124. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  125. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  126. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  127. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  128. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  129. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  130. test/new-results/multi-annotate-new-simu.yaml +1 -0
  131. test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
  132. test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
  133. test/new-results/partition-new-simu/fasttree/iclust-0/log +23 -0
  134. test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
  135. test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
  136. test/new-results/partition-new-simu/fasttree/iclust-1/log +23 -0
  137. test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
  138. test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
  139. test/new-results/partition-new-simu/fasttree/iclust-2/log +22 -0
  140. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  141. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  142. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  143. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  144. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  145. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  146. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  147. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  148. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  149. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  150. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  151. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  152. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  153. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  154. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  155. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  156. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  157. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  158. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  159. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  160. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  161. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  162. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  163. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  164. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  165. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  166. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  167. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  168. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  169. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  170. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  171. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  172. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  173. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  174. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  175. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  176. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  177. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  178. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  179. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  180. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  181. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  182. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  183. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  184. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  185. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  186. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  187. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  188. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  189. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  190. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  191. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  192. test/new-results/partition-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  193. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  194. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  195. test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  196. test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
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  634. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  635. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  636. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  637. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  638. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  639. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  640. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/data/hmm/hmms/IGHJ3_star_02.yaml ADDED
@@ -0,0 +1,946 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.10869565217391304
4
+ overall_mute_freq: 0.08760869565217394
5
+ per_gene_mute_freq: 0.12517826293769102
6
+ name: IGHJ3_star_02
7
+ states:
8
+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
11
+ name: init
12
+ transitions:
13
+ IGHJ3_star_02_0: 0.005555555555555555
14
+ IGHJ3_star_02_1: 0.006481481481481481
15
+ IGHJ3_star_02_10: 0.0027777777777777775
16
+ IGHJ3_star_02_11: 0.0027777777777777775
17
+ IGHJ3_star_02_12: 0.0027777777777777775
18
+ IGHJ3_star_02_13: 0.0027777777777777775
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+ IGHJ3_star_02_14: 0.0027777777777777775
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+ IGHJ3_star_02_15: 0.0027777777777777775
21
+ IGHJ3_star_02_16: 0.0027777777777777775
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+ IGHJ3_star_02_2: 0.007407407407407407
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+ IGHJ3_star_02_3: 0.008333333333333333
24
+ IGHJ3_star_02_4: 0.005555555555555555
25
+ IGHJ3_star_02_5: 0.0027777777777777775
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+ IGHJ3_star_02_6: 0.0027777777777777775
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+ IGHJ3_star_02_7: 0.0027777777777777775
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+ IGHJ3_star_02_8: 0.0027777777777777775
29
+ IGHJ3_star_02_9: 0.0027777777777777775
30
+ insert_left_A: 0.1879194630872483
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+ insert_left_C: 0.2912751677852349
32
+ insert_left_G: 0.21610738255033557
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+ insert_left_T: 0.23803131991051457
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+ - !!python/object:python.hmmwriter.State
35
+ emissions:
36
+ probs:
37
+ A: 0.874821737062309
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+ C: 0.041726087645897005
39
+ G: 0.041726087645897005
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+ T: 0.041726087645897005
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
44
+ ambiguous_emission_prob: 0.25
45
+ germline: A
46
+ name: insert_left_A
47
+ transitions:
48
+ IGHJ3_star_02_0: 0.015822784810126573
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+ IGHJ3_star_02_1: 0.018459915611814336
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+ IGHJ3_star_02_10: 0.007911392405063286
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+ IGHJ3_star_02_11: 0.007911392405063286
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+ IGHJ3_star_02_12: 0.007911392405063286
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+ IGHJ3_star_02_13: 0.007911392405063286
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+ IGHJ3_star_02_14: 0.007911392405063286
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+ IGHJ3_star_02_15: 0.007911392405063286
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+ IGHJ3_star_02_16: 0.007911392405063286
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+ IGHJ3_star_02_2: 0.0210970464135021
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+ IGHJ3_star_02_3: 0.02373417721518986
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+ IGHJ3_star_02_4: 0.015822784810126573
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+ IGHJ3_star_02_5: 0.007911392405063286
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+ IGHJ3_star_02_6: 0.007911392405063286
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+ IGHJ3_star_02_7: 0.007911392405063286
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+ IGHJ3_star_02_8: 0.007911392405063286
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+ IGHJ3_star_02_9: 0.007911392405063286
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+ insert_left_A: 0.16311273468694248
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+ insert_left_C: 0.25282473876476086
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+ insert_left_G: 0.18757964488998388
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+ insert_left_T: 0.20660946393679386
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
71
+ probs:
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+ A: 0.041726087645897005
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+ C: 0.874821737062309
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+ G: 0.041726087645897005
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+ T: 0.041726087645897005
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+ track: nukes
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+ 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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+ IGHJ3_star_02_0: 0.015822784810126573
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+ IGHJ3_star_02_1: 0.018459915611814336
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+ IGHJ3_star_02_10: 0.007911392405063286
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+ IGHJ3_star_02_11: 0.007911392405063286
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+ IGHJ3_star_02_12: 0.007911392405063286
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+ IGHJ3_star_02_13: 0.007911392405063286
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+ IGHJ3_star_02_14: 0.007911392405063286
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+ IGHJ3_star_02_15: 0.007911392405063286
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+ IGHJ3_star_02_16: 0.007911392405063286
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+ IGHJ3_star_02_2: 0.0210970464135021
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+ IGHJ3_star_02_3: 0.02373417721518986
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+ IGHJ3_star_02_4: 0.015822784810126573
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+ IGHJ3_star_02_5: 0.007911392405063286
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+ IGHJ3_star_02_6: 0.007911392405063286
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+ IGHJ3_star_02_7: 0.007911392405063286
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+ IGHJ3_star_02_8: 0.007911392405063286
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+ IGHJ3_star_02_9: 0.007911392405063286
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+ insert_left_A: 0.16311273468694248
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+ insert_left_C: 0.25282473876476086
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+ insert_left_G: 0.18757964488998388
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+ insert_left_T: 0.20660946393679386
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+ - !!python/object:python.hmmwriter.State
105
+ emissions:
106
+ probs:
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+ A: 0.041726087645897005
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+ C: 0.041726087645897005
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+ G: 0.874821737062309
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+ T: 0.041726087645897005
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
114
+ ambiguous_emission_prob: 0.25
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+ germline: G
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+ name: insert_left_G
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+ transitions:
118
+ IGHJ3_star_02_0: 0.015822784810126573
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+ IGHJ3_star_02_1: 0.018459915611814336
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+ IGHJ3_star_02_10: 0.007911392405063286
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+ IGHJ3_star_02_11: 0.007911392405063286
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+ IGHJ3_star_02_12: 0.007911392405063286
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+ IGHJ3_star_02_13: 0.007911392405063286
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+ IGHJ3_star_02_14: 0.007911392405063286
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+ IGHJ3_star_02_15: 0.007911392405063286
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+ IGHJ3_star_02_16: 0.007911392405063286
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+ IGHJ3_star_02_2: 0.0210970464135021
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+ IGHJ3_star_02_3: 0.02373417721518986
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+ IGHJ3_star_02_4: 0.015822784810126573
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+ IGHJ3_star_02_5: 0.007911392405063286
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+ IGHJ3_star_02_6: 0.007911392405063286
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+ IGHJ3_star_02_7: 0.007911392405063286
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+ IGHJ3_star_02_8: 0.007911392405063286
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+ IGHJ3_star_02_9: 0.007911392405063286
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+ insert_left_A: 0.16311273468694248
136
+ insert_left_C: 0.25282473876476086
137
+ insert_left_G: 0.18757964488998388
138
+ insert_left_T: 0.20660946393679386
139
+ - !!python/object:python.hmmwriter.State
140
+ emissions:
141
+ probs:
142
+ A: 0.041726087645897005
143
+ C: 0.041726087645897005
144
+ G: 0.041726087645897005
145
+ T: 0.874821737062309
146
+ track: nukes
147
+ extras:
148
+ ambiguous_char: N
149
+ ambiguous_emission_prob: 0.25
150
+ germline: T
151
+ name: insert_left_T
152
+ transitions:
153
+ IGHJ3_star_02_0: 0.015822784810126573
154
+ IGHJ3_star_02_1: 0.018459915611814336
155
+ IGHJ3_star_02_10: 0.007911392405063286
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+ IGHJ3_star_02_11: 0.007911392405063286
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+ IGHJ3_star_02_12: 0.007911392405063286
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+ IGHJ3_star_02_13: 0.007911392405063286
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+ IGHJ3_star_02_14: 0.007911392405063286
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+ IGHJ3_star_02_15: 0.007911392405063286
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+ IGHJ3_star_02_16: 0.007911392405063286
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+ IGHJ3_star_02_2: 0.0210970464135021
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+ IGHJ3_star_02_3: 0.02373417721518986
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+ IGHJ3_star_02_4: 0.015822784810126573
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+ IGHJ3_star_02_5: 0.007911392405063286
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+ IGHJ3_star_02_6: 0.007911392405063286
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+ IGHJ3_star_02_7: 0.007911392405063286
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+ IGHJ3_star_02_8: 0.007911392405063286
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+ IGHJ3_star_02_9: 0.007911392405063286
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+ insert_left_A: 0.16311273468694248
171
+ insert_left_C: 0.25282473876476086
172
+ insert_left_G: 0.18757964488998388
173
+ insert_left_T: 0.20660946393679386
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+ - !!python/object:python.hmmwriter.State
175
+ emissions:
176
+ probs:
177
+ A: 0.041726087645897005
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+ C: 0.041726087645897005
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+ G: 0.041726087645897005
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+ T: 0.874821737062309
181
+ track: nukes
182
+ extras:
183
+ ambiguous_char: N
184
+ ambiguous_emission_prob: 0.25
185
+ germline: T
186
+ name: IGHJ3_star_02_0
187
+ transitions:
188
+ IGHJ3_star_02_1: 1.0
189
+ - !!python/object:python.hmmwriter.State
190
+ emissions:
191
+ probs:
192
+ A: 0.041541201572361325
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+ C: 0.041541201572361325
194
+ G: 0.875376395282916
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+ T: 0.041541201572361325
196
+ track: nukes
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+ extras:
198
+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
200
+ germline: G
201
+ name: IGHJ3_star_02_1
202
+ transitions:
203
+ IGHJ3_star_02_2: 1.0
204
+ - !!python/object:python.hmmwriter.State
205
+ emissions:
206
+ probs:
207
+ A: 0.8748395633560782
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+ C: 0.041720145547973965
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+ T: 0.041720145547973965
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
214
+ ambiguous_emission_prob: 0.25
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+ germline: A
216
+ name: IGHJ3_star_02_2
217
+ transitions:
218
+ IGHJ3_star_02_3: 1.0
219
+ - !!python/object:python.hmmwriter.State
220
+ emissions:
221
+ probs:
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+ A: 0.04171717449901245
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+ C: 0.04171717449901245
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+ T: 0.8748484765029626
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: T
231
+ name: IGHJ3_star_02_3
232
+ transitions:
233
+ IGHJ3_star_02_4: 1.0
234
+ - !!python/object:python.hmmwriter.State
235
+ emissions:
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+ A: 0.04171420345005093
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+ C: 0.04171420345005093
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+ T: 0.04171420345005093
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
245
+ germline: G
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+ name: IGHJ3_star_02_4
247
+ transitions:
248
+ IGHJ3_star_02_5: 1.0
249
+ - !!python/object:python.hmmwriter.State
250
+ emissions:
251
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+ A: 0.04171123240108941
253
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254
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+ T: 0.04171123240108941
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+ track: nukes
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+ 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: IGHJ3_star_02_5
262
+ transitions:
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+ IGHJ3_star_02_6: 1.0
264
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_char: N
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+ germline: T
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+ name: IGHJ3_star_02_6
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+ transitions:
278
+ IGHJ3_star_02_7: 1.0
279
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_char: N
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+ germline: T
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+ name: IGHJ3_star_02_7
292
+ transitions:
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+ IGHJ3_star_02_8: 1.0
294
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_char: N
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+ germline: T
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+ name: IGHJ3_star_02_8
307
+ transitions:
308
+ IGHJ3_star_02_9: 1.0
309
+ - !!python/object:python.hmmwriter.State
310
+ emissions:
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+ name: IGHJ3_star_02_9
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+ transitions:
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+ IGHJ3_star_02_10: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ germline: G
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+ name: IGHJ3_star_02_10
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+ transitions:
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+ IGHJ3_star_02_11: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHJ3_star_02_11
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+ transitions:
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHJ3_star_02_12
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+ transitions:
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+ IGHJ3_star_02_13: 1.0
369
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHJ3_star_02_13
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+ - !!python/object:python.hmmwriter.State
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHJ3_star_02_15
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+ transitions:
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+ IGHJ3_star_02_16: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHJ3_star_02_16
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+ IGHJ3_star_02_17: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ - !!python/object:python.hmmwriter.State
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