partis-bcr 1.0.11.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl → 1.0.12__cp312-cp312-macosx_10_13_universal2.whl

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Files changed (647) 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-1.0.12.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/RECORD +647 -129
  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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  633. test/paired/new-results/test.log +142 -133
  634. test/test.py +6 -0
  635. test/trees.nwk +100 -0
  636. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/cf-alleles.py +0 -0
  637. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/cf-germlines.py +0 -0
  638. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/compare-plotdirs.py +0 -0
  639. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/extract-pairing-info.py +0 -0
  640. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/gctree-run.py +0 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/get-naive-probabilities.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/parse-output.py +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/split-loci.py +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/WHEEL +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/entry_points.txt +0 -0
  646. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/licenses/COPYING +0 -0
  647. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/data/hmm/hmms/IGHD4-17_star_01.yaml ADDED
@@ -0,0 +1,429 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.043478260869565216
4
+ overall_mute_freq: 0.08760869565217394
5
+ per_gene_mute_freq: 0.10955699500874688
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+ name: IGHD4-17_star_01
7
+ states:
8
+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
11
+ name: init
12
+ transitions:
13
+ IGHD4-17_star_01_0: 0.01282051282051282
14
+ IGHD4-17_star_01_1: 0.01282051282051282
15
+ IGHD4-17_star_01_10: 7.11681426041767e-19
16
+ IGHD4-17_star_01_11: 0.01282051282051282
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+ IGHD4-17_star_01_12: 0.01282051282051282
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+ IGHD4-17_star_01_13: 0.01282051282051282
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+ IGHD4-17_star_01_14: 0.01282051282051282
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+ IGHD4-17_star_01_15: 0.01282051282051282
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+ IGHD4-17_star_01_2: 0.01282051282051282
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+ IGHD4-17_star_01_3: 0.01282051282051282
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+ IGHD4-17_star_01_4: 0.01282051282051282
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+ IGHD4-17_star_01_5: 0.01282051282051282
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+ IGHD4-17_star_01_6: 0.010256410256410256
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+ IGHD4-17_star_01_7: 0.007692307692307694
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+ IGHD4-17_star_01_8: 0.005128205128205129
28
+ IGHD4-17_star_01_9: 0.0025641025641025645
29
+ insert_left_A: 0.15664160401002505
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+ insert_left_C: 0.2819548872180451
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+ insert_left_G: 0.19423558897243107
32
+ insert_left_T: 0.20050125313283207
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+ - !!python/object:python.hmmwriter.State
34
+ emissions:
35
+ probs:
36
+ A: 0.8904430049912531
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+ C: 0.03651899833624896
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+ G: 0.03651899833624896
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+ T: 0.03651899833624896
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
43
+ ambiguous_emission_prob: 0.25
44
+ germline: A
45
+ name: insert_left_A
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+ transitions:
47
+ IGHD4-17_star_01_0: 0.030769230769230764
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+ IGHD4-17_star_01_1: 0.030769230769230764
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+ IGHD4-17_star_01_10: 1.7080354225002405e-18
50
+ IGHD4-17_star_01_11: 0.030769230769230764
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+ IGHD4-17_star_01_12: 0.030769230769230764
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+ IGHD4-17_star_01_13: 0.030769230769230764
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+ IGHD4-17_star_01_14: 0.030769230769230764
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+ IGHD4-17_star_01_15: 0.030769230769230764
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+ IGHD4-17_star_01_2: 0.030769230769230764
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+ IGHD4-17_star_01_3: 0.030769230769230764
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+ IGHD4-17_star_01_4: 0.030769230769230764
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+ IGHD4-17_star_01_5: 0.030769230769230764
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+ IGHD4-17_star_01_6: 0.024615384615384612
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+ IGHD4-17_star_01_7: 0.01846153846153846
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+ IGHD4-17_star_01_8: 0.012307692307692308
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+ IGHD4-17_star_01_9: 0.006153846153846154
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+ insert_left_A: 0.11278195488721805
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+ insert_left_C: 0.2030075187969925
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+ insert_left_G: 0.1398496240601504
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+ insert_left_T: 0.1443609022556391
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
69
+ probs:
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+ A: 0.03651899833624896
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+ C: 0.8904430049912531
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+ G: 0.03651899833624896
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+ T: 0.03651899833624896
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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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+ IGHD4-17_star_01_0: 0.030769230769230764
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+ IGHD4-17_star_01_1: 0.030769230769230764
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+ IGHD4-17_star_01_10: 1.7080354225002405e-18
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+ IGHD4-17_star_01_11: 0.030769230769230764
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+ IGHD4-17_star_01_12: 0.030769230769230764
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+ IGHD4-17_star_01_13: 0.030769230769230764
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+ IGHD4-17_star_01_14: 0.030769230769230764
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+ IGHD4-17_star_01_15: 0.030769230769230764
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+ IGHD4-17_star_01_2: 0.030769230769230764
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+ IGHD4-17_star_01_3: 0.030769230769230764
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+ IGHD4-17_star_01_4: 0.030769230769230764
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+ IGHD4-17_star_01_5: 0.030769230769230764
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+ IGHD4-17_star_01_6: 0.024615384615384612
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+ IGHD4-17_star_01_7: 0.01846153846153846
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+ IGHD4-17_star_01_8: 0.012307692307692308
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+ IGHD4-17_star_01_9: 0.006153846153846154
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+ insert_left_A: 0.11278195488721805
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+ insert_left_C: 0.2030075187969925
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+ insert_left_G: 0.1398496240601504
100
+ insert_left_T: 0.1443609022556391
101
+ - !!python/object:python.hmmwriter.State
102
+ emissions:
103
+ probs:
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+ A: 0.03651899833624896
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+ C: 0.03651899833624896
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+ G: 0.8904430049912531
107
+ T: 0.03651899833624896
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+ track: nukes
109
+ extras:
110
+ ambiguous_char: N
111
+ ambiguous_emission_prob: 0.25
112
+ germline: G
113
+ name: insert_left_G
114
+ transitions:
115
+ IGHD4-17_star_01_0: 0.030769230769230764
116
+ IGHD4-17_star_01_1: 0.030769230769230764
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+ IGHD4-17_star_01_10: 1.7080354225002405e-18
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+ IGHD4-17_star_01_11: 0.030769230769230764
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+ IGHD4-17_star_01_12: 0.030769230769230764
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+ IGHD4-17_star_01_13: 0.030769230769230764
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+ IGHD4-17_star_01_14: 0.030769230769230764
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+ IGHD4-17_star_01_15: 0.030769230769230764
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+ IGHD4-17_star_01_2: 0.030769230769230764
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+ IGHD4-17_star_01_3: 0.030769230769230764
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+ IGHD4-17_star_01_4: 0.030769230769230764
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+ IGHD4-17_star_01_5: 0.030769230769230764
127
+ IGHD4-17_star_01_6: 0.024615384615384612
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+ IGHD4-17_star_01_7: 0.01846153846153846
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+ IGHD4-17_star_01_8: 0.012307692307692308
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+ IGHD4-17_star_01_9: 0.006153846153846154
131
+ insert_left_A: 0.11278195488721805
132
+ insert_left_C: 0.2030075187969925
133
+ insert_left_G: 0.1398496240601504
134
+ insert_left_T: 0.1443609022556391
135
+ - !!python/object:python.hmmwriter.State
136
+ emissions:
137
+ probs:
138
+ A: 0.03651899833624896
139
+ C: 0.03651899833624896
140
+ G: 0.03651899833624896
141
+ T: 0.8904430049912531
142
+ track: nukes
143
+ extras:
144
+ ambiguous_char: N
145
+ ambiguous_emission_prob: 0.25
146
+ germline: T
147
+ name: insert_left_T
148
+ transitions:
149
+ IGHD4-17_star_01_0: 0.030769230769230764
150
+ IGHD4-17_star_01_1: 0.030769230769230764
151
+ IGHD4-17_star_01_10: 1.7080354225002405e-18
152
+ IGHD4-17_star_01_11: 0.030769230769230764
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+ IGHD4-17_star_01_12: 0.030769230769230764
154
+ IGHD4-17_star_01_13: 0.030769230769230764
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+ IGHD4-17_star_01_14: 0.030769230769230764
156
+ IGHD4-17_star_01_15: 0.030769230769230764
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+ IGHD4-17_star_01_2: 0.030769230769230764
158
+ IGHD4-17_star_01_3: 0.030769230769230764
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+ IGHD4-17_star_01_4: 0.030769230769230764
160
+ IGHD4-17_star_01_5: 0.030769230769230764
161
+ IGHD4-17_star_01_6: 0.024615384615384612
162
+ IGHD4-17_star_01_7: 0.01846153846153846
163
+ IGHD4-17_star_01_8: 0.012307692307692308
164
+ IGHD4-17_star_01_9: 0.006153846153846154
165
+ insert_left_A: 0.11278195488721805
166
+ insert_left_C: 0.2030075187969925
167
+ insert_left_G: 0.1398496240601504
168
+ insert_left_T: 0.1443609022556391
169
+ - !!python/object:python.hmmwriter.State
170
+ emissions:
171
+ probs:
172
+ A: 0.036518998336248956
173
+ C: 0.036518998336248956
174
+ G: 0.036518998336248956
175
+ T: 0.8904430049912531
176
+ track: nukes
177
+ extras:
178
+ ambiguous_char: N
179
+ ambiguous_emission_prob: 0.25
180
+ germline: T
181
+ name: IGHD4-17_star_01_0
182
+ transitions:
183
+ IGHD4-17_star_01_1: 0.935483870967742
184
+ end: 0.06451612903225806
185
+ - !!python/object:python.hmmwriter.State
186
+ emissions:
187
+ probs:
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+ A: 0.03616503555814722
189
+ C: 0.03616503555814722
190
+ G: 0.8915048933255583
191
+ T: 0.03616503555814722
192
+ track: nukes
193
+ extras:
194
+ ambiguous_char: N
195
+ ambiguous_emission_prob: 0.25
196
+ germline: G
197
+ name: IGHD4-17_star_01_1
198
+ transitions:
199
+ IGHD4-17_star_01_2: 0.935483870967742
200
+ end: 0.06451612903225806
201
+ - !!python/object:python.hmmwriter.State
202
+ emissions:
203
+ probs:
204
+ A: 0.8925667816598636
205
+ C: 0.035811072780045486
206
+ G: 0.035811072780045486
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+ T: 0.035811072780045486
208
+ track: nukes
209
+ extras:
210
+ ambiguous_char: N
211
+ ambiguous_emission_prob: 0.25
212
+ germline: A
213
+ name: IGHD4-17_star_01_2
214
+ transitions:
215
+ IGHD4-17_star_01_3: 0.935483870967742
216
+ end: 0.06451612903225806
217
+ - !!python/object:python.hmmwriter.State
218
+ emissions:
219
+ probs:
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+ A: 0.03545711000194375
221
+ C: 0.8936286699941687
222
+ G: 0.03545711000194375
223
+ T: 0.03545711000194375
224
+ track: nukes
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+ extras:
226
+ ambiguous_char: N
227
+ ambiguous_emission_prob: 0.25
228
+ germline: C
229
+ name: IGHD4-17_star_01_3
230
+ transitions:
231
+ IGHD4-17_star_01_4: 0.935483870967742
232
+ end: 0.06451612903225806
233
+ - !!python/object:python.hmmwriter.State
234
+ emissions:
235
+ probs:
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+ A: 0.036231379219067945
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+ C: 0.036231379219067945
238
+ G: 0.036231379219067945
239
+ T: 0.8913058623427962
240
+ track: nukes
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+ extras:
242
+ ambiguous_char: N
243
+ ambiguous_emission_prob: 0.25
244
+ germline: T
245
+ name: IGHD4-17_star_01_4
246
+ transitions:
247
+ IGHD4-17_star_01_5: 0.935483870967742
248
+ end: 0.06451612903225806
249
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ C: 0.037357536024545834
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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
260
+ germline: A
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+ name: IGHD4-17_star_01_5
262
+ transitions:
263
+ IGHD4-17_star_01_6: 0.935483870967742
264
+ end: 0.06451612903225806
265
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
275
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+ germline: C
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+ name: IGHD4-17_star_01_6
278
+ transitions:
279
+ IGHD4-17_star_01_7: 0.935483870967742
280
+ end: 0.06451612903225806
281
+ - !!python/object:python.hmmwriter.State
282
+ emissions:
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+ track: nukes
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+ extras:
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291
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+ germline: G
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+ name: IGHD4-17_star_01_7
294
+ transitions:
295
+ IGHD4-17_star_01_8: 0.935483870967742
296
+ end: 0.06451612903225806
297
+ - !!python/object:python.hmmwriter.State
298
+ emissions:
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+ germline: G
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+ name: IGHD4-17_star_01_8
310
+ transitions:
311
+ IGHD4-17_star_01_9: 0.935483870967742
312
+ end: 0.06451612903225806
313
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHD4-17_star_01_9
326
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+ IGHD4-17_star_01_10: 0.935483870967742
328
+ end: 0.06451612903225806
329
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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342
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344
+ end: 0.06451612903225806
345
+ - !!python/object:python.hmmwriter.State
346
+ emissions:
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355
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+ germline: A
357
+ name: IGHD4-17_star_01_11
358
+ transitions:
359
+ IGHD4-17_star_01_12: 0.935483870967742
360
+ end: 0.06451612903225806
361
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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371
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373
+ name: IGHD4-17_star_01_12
374
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376
+ end: 0.03225806451612903
377
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHD4-17_star_01_13
390
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391
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392
+ end: 0.06451612903225806
393
+ - !!python/object:python.hmmwriter.State
394
+ emissions:
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403
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406
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407
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408
+ end: 0.06451612903225806
409
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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422
+ transitions:
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+ end: 1.0
424
+ tracks:
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426
+ - A
427
+ - C
428
+ - G
429
+ - T