partis-bcr 1.0.11.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.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 (652) 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.dev3.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/RECORD +652 -125
  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. test/paired/new-results/test/simu/igh+igl/igl.yaml +1 -0
  635. test/paired/new-results/test/simu/igh.yaml +1 -0
  636. test/paired/new-results/test/simu/igk.yaml +1 -0
  637. test/paired/new-results/test/simu/igl.yaml +1 -0
  638. test/paired/new-results/test/simu/meta.yaml +1 -0
  639. test/paired/new-results/test.log +227 -33
  640. test/test.py +6 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/gctree-run.py +0 -0
  646. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  647. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/parse-output.py +0 -0
  648. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/split-loci.py +0 -0
  649. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/WHEEL +0 -0
  650. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/entry_points.txt +0 -0
  651. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/licenses/COPYING +0 -0
  652. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/sw/hmms/IGHD6-13_star_01.yaml CHANGED
@@ -1,8 +1,8 @@
1
1
  !!python/object:python.hmmwriter.HMM
2
2
  extras:
3
- gene_prob: 1.0
4
- overall_mute_freq: 0.019000000000000003
5
- per_gene_mute_freq: 0.10789436745220951
3
+ gene_prob: 0.6388888888888888
4
+ overall_mute_freq: 0.012222222222222223
5
+ per_gene_mute_freq: 0.07742066644916665
6
6
  name: IGHD6-13_star_01
7
7
  states:
8
8
  - !!python/object:python.hmmwriter.State
@@ -10,38 +10,38 @@ states:
10
10
  extras: {}
11
11
  name: init
12
12
  transitions:
13
- IGHD6-13_star_01_0: 0.0019047619047619048
14
- IGHD6-13_star_01_1: 0.0019047619047619048
15
- IGHD6-13_star_01_10: 0.0050793650793650785
16
- IGHD6-13_star_01_11: 0.004444444444444444
17
- IGHD6-13_star_01_12: 0.003809523809523809
18
- IGHD6-13_star_01_13: 0.003174603174603174
19
- IGHD6-13_star_01_14: 0.0025396825396825392
20
- IGHD6-13_star_01_15: 0.0019047619047619048
21
- IGHD6-13_star_01_16: 0.0012698412698412698
22
- IGHD6-13_star_01_17: 0.0006349206349206351
23
- IGHD6-13_star_01_18: 2.1147105230955363e-19
24
- IGHD6-13_star_01_19: 0.0019047619047619048
25
- IGHD6-13_star_01_2: 0.0019047619047619048
26
- IGHD6-13_star_01_20: 0.0019047619047619048
27
- IGHD6-13_star_01_3: 0.011428571428571429
28
- IGHD6-13_star_01_4: 0.0019047619047619048
29
- IGHD6-13_star_01_5: 0.0026666666666666666
30
- IGHD6-13_star_01_6: 0.003428571428571429
31
- IGHD6-13_star_01_7: 0.004190476190476191
32
- IGHD6-13_star_01_8: 0.004952380952380953
33
- IGHD6-13_star_01_9: 0.005714285714285714
34
- insert_left_A: 0.08484848484848485
35
- insert_left_C: 0.39595959595959596
36
- insert_left_G: 0.1696969696969697
37
- insert_left_T: 0.2828282828282828
13
+ IGHD6-13_star_01_0: 0.00045913682277318646
14
+ IGHD6-13_star_01_1: 0.002066115702479339
15
+ IGHD6-13_star_01_10: 0.001224364860728497
16
+ IGHD6-13_star_01_11: 0.0010713192531374349
17
+ IGHD6-13_star_01_12: 0.0009182736455463728
18
+ IGHD6-13_star_01_13: 0.0007652280379553107
19
+ IGHD6-13_star_01_14: 0.0006121824303642485
20
+ IGHD6-13_star_01_15: 0.00045913682277318646
21
+ IGHD6-13_star_01_16: 0.0003060912151821243
22
+ IGHD6-13_star_01_17: 0.00015304560759106216
23
+ IGHD6-13_star_01_18: 5.097442720960315e-20
24
+ IGHD6-13_star_01_19: 0.00045913682277318646
25
+ IGHD6-13_star_01_2: 0.0036730945821854917
26
+ IGHD6-13_star_01_20: 0.00045913682277318646
27
+ IGHD6-13_star_01_3: 0.004591368227731864
28
+ IGHD6-13_star_01_4: 0.00045913682277318646
29
+ IGHD6-13_star_01_5: 0.0006427915518824609
30
+ IGHD6-13_star_01_6: 0.0008264462809917356
31
+ IGHD6-13_star_01_7: 0.00101010101010101
32
+ IGHD6-13_star_01_8: 0.001193755739210285
33
+ IGHD6-13_star_01_9: 0.0013774104683195593
34
+ insert_left_A: 0.1213166144200627
35
+ insert_left_C: 0.43134796238244516
36
+ insert_left_G: 0.16849529780564265
37
+ insert_left_T: 0.25611285266457684
38
38
  - !!python/object:python.hmmwriter.State
39
39
  emissions:
40
40
  probs:
41
- A: 0.8921056325477905
42
- C: 0.035964789150736504
43
- G: 0.035964789150736504
44
- T: 0.035964789150736504
41
+ A: 0.9225793335508333
42
+ C: 0.025806888816388884
43
+ G: 0.025806888816388884
44
+ T: 0.025806888816388884
45
45
  track: nukes
46
46
  extras:
47
47
  ambiguous_char: N
@@ -49,38 +49,38 @@ states:
49
49
  germline: A
50
50
  name: insert_left_A
51
51
  transitions:
52
- IGHD6-13_star_01_0: 0.008348794063079779
53
- IGHD6-13_star_01_1: 0.008348794063079779
54
- IGHD6-13_star_01_10: 0.022263450834879406
55
- IGHD6-13_star_01_11: 0.01948051948051948
56
- IGHD6-13_star_01_12: 0.016697588126159554
57
- IGHD6-13_star_01_13: 0.01391465677179963
58
- IGHD6-13_star_01_14: 0.011131725417439703
59
- IGHD6-13_star_01_15: 0.008348794063079779
60
- IGHD6-13_star_01_16: 0.005565862708719853
61
- IGHD6-13_star_01_17: 0.002782931354359927
62
- IGHD6-13_star_01_18: 9.269023396684982e-19
63
- IGHD6-13_star_01_19: 0.008348794063079779
64
- IGHD6-13_star_01_2: 0.008348794063079779
65
- IGHD6-13_star_01_20: 0.008348794063079779
66
- IGHD6-13_star_01_3: 0.05009276437847867
67
- IGHD6-13_star_01_4: 0.008348794063079779
68
- IGHD6-13_star_01_5: 0.01168831168831169
69
- IGHD6-13_star_01_6: 0.015027829313543604
70
- IGHD6-13_star_01_7: 0.018367346938775515
71
- IGHD6-13_star_01_8: 0.021706864564007423
72
- IGHD6-13_star_01_9: 0.025046382189239335
73
- insert_left_A: 0.06434474616292798
74
- insert_left_C: 0.3002754820936639
75
- insert_left_G: 0.12868949232585597
76
- insert_left_T: 0.21448248720975993
52
+ IGHD6-13_star_01_0: 0.002904865649963688
53
+ IGHD6-13_star_01_1: 0.013071895424836595
54
+ IGHD6-13_star_01_10: 0.007746308399903167
55
+ IGHD6-13_star_01_11: 0.006778019849915271
56
+ IGHD6-13_star_01_12: 0.005809731299927375
57
+ IGHD6-13_star_01_13: 0.00484144274993948
58
+ IGHD6-13_star_01_14: 0.0038731541999515837
59
+ IGHD6-13_star_01_15: 0.002904865649963688
60
+ IGHD6-13_star_01_16: 0.001936577099975792
61
+ IGHD6-13_star_01_17: 0.0009682885499878961
62
+ IGHD6-13_star_01_18: 3.225048728032407e-19
63
+ IGHD6-13_star_01_19: 0.002904865649963688
64
+ IGHD6-13_star_01_2: 0.023238925199709503
65
+ IGHD6-13_star_01_20: 0.002904865649963688
66
+ IGHD6-13_star_01_3: 0.029048656499636876
67
+ IGHD6-13_star_01_4: 0.002904865649963688
68
+ IGHD6-13_star_01_5: 0.004066811909949163
69
+ IGHD6-13_star_01_6: 0.005228758169934638
70
+ IGHD6-13_star_01_7: 0.006390704429920113
71
+ IGHD6-13_star_01_8: 0.007552650689905589
72
+ IGHD6-13_star_01_9: 0.008714596949891063
73
+ insert_left_A: 0.10628803245436107
74
+ insert_left_C: 0.37791300428217267
75
+ insert_left_G: 0.1476222672977237
76
+ insert_left_T: 0.22438584629254005
77
77
  - !!python/object:python.hmmwriter.State
78
78
  emissions:
79
79
  probs:
80
- A: 0.035964789150736504
81
- C: 0.8921056325477905
82
- G: 0.035964789150736504
83
- T: 0.035964789150736504
80
+ A: 0.025806888816388884
81
+ C: 0.9225793335508333
82
+ G: 0.025806888816388884
83
+ T: 0.025806888816388884
84
84
  track: nukes
85
85
  extras:
86
86
  ambiguous_char: N
@@ -88,38 +88,38 @@ states:
88
88
  germline: C
89
89
  name: insert_left_C
90
90
  transitions:
91
- IGHD6-13_star_01_0: 0.008348794063079779
92
- IGHD6-13_star_01_1: 0.008348794063079779
93
- IGHD6-13_star_01_10: 0.022263450834879406
94
- IGHD6-13_star_01_11: 0.01948051948051948
95
- IGHD6-13_star_01_12: 0.016697588126159554
96
- IGHD6-13_star_01_13: 0.01391465677179963
97
- IGHD6-13_star_01_14: 0.011131725417439703
98
- IGHD6-13_star_01_15: 0.008348794063079779
99
- IGHD6-13_star_01_16: 0.005565862708719853
100
- IGHD6-13_star_01_17: 0.002782931354359927
101
- IGHD6-13_star_01_18: 9.269023396684982e-19
102
- IGHD6-13_star_01_19: 0.008348794063079779
103
- IGHD6-13_star_01_2: 0.008348794063079779
104
- IGHD6-13_star_01_20: 0.008348794063079779
105
- IGHD6-13_star_01_3: 0.05009276437847867
106
- IGHD6-13_star_01_4: 0.008348794063079779
107
- IGHD6-13_star_01_5: 0.01168831168831169
108
- IGHD6-13_star_01_6: 0.015027829313543604
109
- IGHD6-13_star_01_7: 0.018367346938775515
110
- IGHD6-13_star_01_8: 0.021706864564007423
111
- IGHD6-13_star_01_9: 0.025046382189239335
112
- insert_left_A: 0.06434474616292798
113
- insert_left_C: 0.3002754820936639
114
- insert_left_G: 0.12868949232585597
115
- insert_left_T: 0.21448248720975993
91
+ IGHD6-13_star_01_0: 0.002904865649963688
92
+ IGHD6-13_star_01_1: 0.013071895424836595
93
+ IGHD6-13_star_01_10: 0.007746308399903167
94
+ IGHD6-13_star_01_11: 0.006778019849915271
95
+ IGHD6-13_star_01_12: 0.005809731299927375
96
+ IGHD6-13_star_01_13: 0.00484144274993948
97
+ IGHD6-13_star_01_14: 0.0038731541999515837
98
+ IGHD6-13_star_01_15: 0.002904865649963688
99
+ IGHD6-13_star_01_16: 0.001936577099975792
100
+ IGHD6-13_star_01_17: 0.0009682885499878961
101
+ IGHD6-13_star_01_18: 3.225048728032407e-19
102
+ IGHD6-13_star_01_19: 0.002904865649963688
103
+ IGHD6-13_star_01_2: 0.023238925199709503
104
+ IGHD6-13_star_01_20: 0.002904865649963688
105
+ IGHD6-13_star_01_3: 0.029048656499636876
106
+ IGHD6-13_star_01_4: 0.002904865649963688
107
+ IGHD6-13_star_01_5: 0.004066811909949163
108
+ IGHD6-13_star_01_6: 0.005228758169934638
109
+ IGHD6-13_star_01_7: 0.006390704429920113
110
+ IGHD6-13_star_01_8: 0.007552650689905589
111
+ IGHD6-13_star_01_9: 0.008714596949891063
112
+ insert_left_A: 0.10628803245436107
113
+ insert_left_C: 0.37791300428217267
114
+ insert_left_G: 0.1476222672977237
115
+ insert_left_T: 0.22438584629254005
116
116
  - !!python/object:python.hmmwriter.State
117
117
  emissions:
118
118
  probs:
119
- A: 0.035964789150736504
120
- C: 0.035964789150736504
121
- G: 0.8921056325477905
122
- T: 0.035964789150736504
119
+ A: 0.025806888816388884
120
+ C: 0.025806888816388884
121
+ G: 0.9225793335508333
122
+ T: 0.025806888816388884
123
123
  track: nukes
124
124
  extras:
125
125
  ambiguous_char: N
@@ -127,38 +127,38 @@ states:
127
127
  germline: G
128
128
  name: insert_left_G
129
129
  transitions:
130
- IGHD6-13_star_01_0: 0.008348794063079779
131
- IGHD6-13_star_01_1: 0.008348794063079779
132
- IGHD6-13_star_01_10: 0.022263450834879406
133
- IGHD6-13_star_01_11: 0.01948051948051948
134
- IGHD6-13_star_01_12: 0.016697588126159554
135
- IGHD6-13_star_01_13: 0.01391465677179963
136
- IGHD6-13_star_01_14: 0.011131725417439703
137
- IGHD6-13_star_01_15: 0.008348794063079779
138
- IGHD6-13_star_01_16: 0.005565862708719853
139
- IGHD6-13_star_01_17: 0.002782931354359927
140
- IGHD6-13_star_01_18: 9.269023396684982e-19
141
- IGHD6-13_star_01_19: 0.008348794063079779
142
- IGHD6-13_star_01_2: 0.008348794063079779
143
- IGHD6-13_star_01_20: 0.008348794063079779
144
- IGHD6-13_star_01_3: 0.05009276437847867
145
- IGHD6-13_star_01_4: 0.008348794063079779
146
- IGHD6-13_star_01_5: 0.01168831168831169
147
- IGHD6-13_star_01_6: 0.015027829313543604
148
- IGHD6-13_star_01_7: 0.018367346938775515
149
- IGHD6-13_star_01_8: 0.021706864564007423
150
- IGHD6-13_star_01_9: 0.025046382189239335
151
- insert_left_A: 0.06434474616292798
152
- insert_left_C: 0.3002754820936639
153
- insert_left_G: 0.12868949232585597
154
- insert_left_T: 0.21448248720975993
130
+ IGHD6-13_star_01_0: 0.002904865649963688
131
+ IGHD6-13_star_01_1: 0.013071895424836595
132
+ IGHD6-13_star_01_10: 0.007746308399903167
133
+ IGHD6-13_star_01_11: 0.006778019849915271
134
+ IGHD6-13_star_01_12: 0.005809731299927375
135
+ IGHD6-13_star_01_13: 0.00484144274993948
136
+ IGHD6-13_star_01_14: 0.0038731541999515837
137
+ IGHD6-13_star_01_15: 0.002904865649963688
138
+ IGHD6-13_star_01_16: 0.001936577099975792
139
+ IGHD6-13_star_01_17: 0.0009682885499878961
140
+ IGHD6-13_star_01_18: 3.225048728032407e-19
141
+ IGHD6-13_star_01_19: 0.002904865649963688
142
+ IGHD6-13_star_01_2: 0.023238925199709503
143
+ IGHD6-13_star_01_20: 0.002904865649963688
144
+ IGHD6-13_star_01_3: 0.029048656499636876
145
+ IGHD6-13_star_01_4: 0.002904865649963688
146
+ IGHD6-13_star_01_5: 0.004066811909949163
147
+ IGHD6-13_star_01_6: 0.005228758169934638
148
+ IGHD6-13_star_01_7: 0.006390704429920113
149
+ IGHD6-13_star_01_8: 0.007552650689905589
150
+ IGHD6-13_star_01_9: 0.008714596949891063
151
+ insert_left_A: 0.10628803245436107
152
+ insert_left_C: 0.37791300428217267
153
+ insert_left_G: 0.1476222672977237
154
+ insert_left_T: 0.22438584629254005
155
155
  - !!python/object:python.hmmwriter.State
156
156
  emissions:
157
157
  probs:
158
- A: 0.035964789150736504
159
- C: 0.035964789150736504
160
- G: 0.035964789150736504
161
- T: 0.8921056325477905
158
+ A: 0.025806888816388884
159
+ C: 0.025806888816388884
160
+ G: 0.025806888816388884
161
+ T: 0.9225793335508333
162
162
  track: nukes
163
163
  extras:
164
164
  ambiguous_char: N
@@ -166,38 +166,38 @@ states:
166
166
  germline: T
167
167
  name: insert_left_T
168
168
  transitions:
169
- IGHD6-13_star_01_0: 0.008348794063079779
170
- IGHD6-13_star_01_1: 0.008348794063079779
171
- IGHD6-13_star_01_10: 0.022263450834879406
172
- IGHD6-13_star_01_11: 0.01948051948051948
173
- IGHD6-13_star_01_12: 0.016697588126159554
174
- IGHD6-13_star_01_13: 0.01391465677179963
175
- IGHD6-13_star_01_14: 0.011131725417439703
176
- IGHD6-13_star_01_15: 0.008348794063079779
177
- IGHD6-13_star_01_16: 0.005565862708719853
178
- IGHD6-13_star_01_17: 0.002782931354359927
179
- IGHD6-13_star_01_18: 9.269023396684982e-19
180
- IGHD6-13_star_01_19: 0.008348794063079779
181
- IGHD6-13_star_01_2: 0.008348794063079779
182
- IGHD6-13_star_01_20: 0.008348794063079779
183
- IGHD6-13_star_01_3: 0.05009276437847867
184
- IGHD6-13_star_01_4: 0.008348794063079779
185
- IGHD6-13_star_01_5: 0.01168831168831169
186
- IGHD6-13_star_01_6: 0.015027829313543604
187
- IGHD6-13_star_01_7: 0.018367346938775515
188
- IGHD6-13_star_01_8: 0.021706864564007423
189
- IGHD6-13_star_01_9: 0.025046382189239335
190
- insert_left_A: 0.06434474616292798
191
- insert_left_C: 0.3002754820936639
192
- insert_left_G: 0.12868949232585597
193
- insert_left_T: 0.21448248720975993
169
+ IGHD6-13_star_01_0: 0.002904865649963688
170
+ IGHD6-13_star_01_1: 0.013071895424836595
171
+ IGHD6-13_star_01_10: 0.007746308399903167
172
+ IGHD6-13_star_01_11: 0.006778019849915271
173
+ IGHD6-13_star_01_12: 0.005809731299927375
174
+ IGHD6-13_star_01_13: 0.00484144274993948
175
+ IGHD6-13_star_01_14: 0.0038731541999515837
176
+ IGHD6-13_star_01_15: 0.002904865649963688
177
+ IGHD6-13_star_01_16: 0.001936577099975792
178
+ IGHD6-13_star_01_17: 0.0009682885499878961
179
+ IGHD6-13_star_01_18: 3.225048728032407e-19
180
+ IGHD6-13_star_01_19: 0.002904865649963688
181
+ IGHD6-13_star_01_2: 0.023238925199709503
182
+ IGHD6-13_star_01_20: 0.002904865649963688
183
+ IGHD6-13_star_01_3: 0.029048656499636876
184
+ IGHD6-13_star_01_4: 0.002904865649963688
185
+ IGHD6-13_star_01_5: 0.004066811909949163
186
+ IGHD6-13_star_01_6: 0.005228758169934638
187
+ IGHD6-13_star_01_7: 0.006390704429920113
188
+ IGHD6-13_star_01_8: 0.007552650689905589
189
+ IGHD6-13_star_01_9: 0.008714596949891063
190
+ insert_left_A: 0.10628803245436107
191
+ insert_left_C: 0.37791300428217267
192
+ insert_left_G: 0.1476222672977237
193
+ insert_left_T: 0.22438584629254005
194
194
  - !!python/object:python.hmmwriter.State
195
195
  emissions:
196
196
  probs:
197
- A: 0.035964789150736504
198
- C: 0.035964789150736504
199
- G: 0.8921056325477905
200
- T: 0.035964789150736504
197
+ A: 0.02580688881638888
198
+ C: 0.02580688881638888
199
+ G: 0.9225793335508333
200
+ T: 0.02580688881638888
201
201
  track: nukes
202
202
  extras:
203
203
  ambiguous_char: N
@@ -205,15 +205,15 @@ states:
205
205
  germline: G
206
206
  name: IGHD6-13_star_01_0
207
207
  transitions:
208
- IGHD6-13_star_01_1: 0.983739837398374
209
- end: 0.016260162601626018
208
+ IGHD6-13_star_01_1: 0.9818181818181818
209
+ end: 0.01818181818181818
210
210
  - !!python/object:python.hmmwriter.State
211
211
  emissions:
212
212
  probs:
213
- A: 0.03567240517102504
214
- C: 0.03567240517102504
215
- G: 0.8929827844869249
216
- T: 0.03567240517102504
213
+ A: 0.026925218428189193
214
+ C: 0.026925218428189193
215
+ G: 0.9192243447154325
216
+ T: 0.026925218428189193
217
217
  track: nukes
218
218
  extras:
219
219
  ambiguous_char: N
@@ -221,15 +221,15 @@ states:
221
221
  germline: G
222
222
  name: IGHD6-13_star_01_1
223
223
  transitions:
224
- IGHD6-13_star_01_2: 0.983739837398374
225
- end: 0.016260162601626018
224
+ IGHD6-13_star_01_2: 0.9818181818181818
225
+ end: 0.01818181818181818
226
226
  - !!python/object:python.hmmwriter.State
227
227
  emissions:
228
228
  probs:
229
- A: 0.035380021191313574
230
- C: 0.035380021191313574
231
- G: 0.8938599364260593
232
- T: 0.035380021191313574
229
+ A: 0.02773156752745987
230
+ C: 0.02773156752745987
231
+ G: 0.9168052974176204
232
+ T: 0.02773156752745987
233
233
  track: nukes
234
234
  extras:
235
235
  ambiguous_char: N
@@ -237,15 +237,15 @@ states:
237
237
  germline: G
238
238
  name: IGHD6-13_star_01_2
239
239
  transitions:
240
- IGHD6-13_star_01_3: 0.983739837398374
241
- end: 0.016260162601626018
240
+ IGHD6-13_star_01_3: 0.9818181818181818
241
+ end: 0.01818181818181818
242
242
  - !!python/object:python.hmmwriter.State
243
243
  emissions:
244
244
  probs:
245
- A: 0.036541116323668785
246
- C: 0.036541116323668785
247
- G: 0.036541116323668785
248
- T: 0.8903766510289937
245
+ A: 0.02389084922598981
246
+ C: 0.02389084922598981
247
+ G: 0.02389084922598981
248
+ T: 0.9283274523220306
249
249
  track: nukes
250
250
  extras:
251
251
  ambiguous_char: N
@@ -253,15 +253,15 @@ states:
253
253
  germline: T
254
254
  name: IGHD6-13_star_01_3
255
255
  transitions:
256
- IGHD6-13_star_01_4: 0.983739837398374
257
- end: 0.016260162601626018
256
+ IGHD6-13_star_01_4: 0.9818181818181818
257
+ end: 0.01818181818181818
258
258
  - !!python/object:python.hmmwriter.State
259
259
  emissions:
260
260
  probs:
261
- A: 0.8910599982012725
262
- C: 0.03631333393290916
263
- G: 0.03631333393290916
264
- T: 0.03631333393290916
261
+ A: 0.9323153110411296
262
+ C: 0.02256156298629012
263
+ G: 0.02256156298629012
264
+ T: 0.02256156298629012
265
265
  track: nukes
266
266
  extras:
267
267
  ambiguous_char: N
@@ -269,15 +269,15 @@ states:
269
269
  germline: A
270
270
  name: IGHD6-13_star_01_4
271
271
  transitions:
272
- IGHD6-13_star_01_5: 0.983739837398374
273
- end: 0.016260162601626018
272
+ IGHD6-13_star_01_5: 0.9818181818181818
273
+ end: 0.01818181818181818
274
274
  - !!python/object:python.hmmwriter.State
275
275
  emissions:
276
276
  probs:
277
- A: 0.03640047012845233
278
- C: 0.03640047012845233
279
- G: 0.03640047012845233
280
- T: 0.890798589614643
277
+ A: 0.02175023152876543
278
+ C: 0.02175023152876543
279
+ G: 0.02175023152876543
280
+ T: 0.9347493054137037
281
281
  track: nukes
282
282
  extras:
283
283
  ambiguous_char: N
@@ -285,15 +285,15 @@ states:
285
285
  germline: T
286
286
  name: IGHD6-13_star_01_5
287
287
  transitions:
288
- IGHD6-13_star_01_6: 0.983739837398374
289
- end: 0.016260162601626018
288
+ IGHD6-13_star_01_6: 0.9818181818181818
289
+ end: 0.01818181818181818
290
290
  - !!python/object:python.hmmwriter.State
291
291
  emissions:
292
292
  probs:
293
- A: 0.8873685441825968
294
- C: 0.03754381860580105
295
- G: 0.03754381860580105
296
- T: 0.03754381860580105
293
+ A: 0.9408597778502777
294
+ C: 0.01971340738324074
295
+ G: 0.01971340738324074
296
+ T: 0.01971340738324074
297
297
  track: nukes
298
298
  extras:
299
299
  ambiguous_char: N
@@ -301,15 +301,14 @@ states:
301
301
  germline: A
302
302
  name: IGHD6-13_star_01_6
303
303
  transitions:
304
- IGHD6-13_star_01_7: 0.983739837398374
305
- end: 0.016260162601626018
304
+ IGHD6-13_star_01_7: 1.0
306
305
  - !!python/object:python.hmmwriter.State
307
306
  emissions:
308
307
  probs:
309
- A: 0.03657474251953867
310
- C: 0.03657474251953867
311
- G: 0.890275772441384
312
- T: 0.03657474251953867
308
+ A: 0.02012756861371605
309
+ C: 0.02012756861371605
310
+ G: 0.9396172941588519
311
+ T: 0.02012756861371605
313
312
  track: nukes
314
313
  extras:
315
314
  ambiguous_char: N
@@ -317,15 +316,15 @@ states:
317
316
  germline: G
318
317
  name: IGHD6-13_star_01_7
319
318
  transitions:
320
- IGHD6-13_star_01_8: 0.983739837398374
321
- end: 0.016260162601626018
319
+ IGHD6-13_star_01_8: 0.9948051948051948
320
+ end: 0.005194805194805203
322
321
  - !!python/object:python.hmmwriter.State
323
322
  emissions:
324
323
  probs:
325
- A: 0.03666187871508183
326
- C: 0.8900143638547545
327
- G: 0.03666187871508183
328
- T: 0.03666187871508183
324
+ A: 0.017682246905524692
325
+ C: 0.9469532592834259
326
+ G: 0.017682246905524692
327
+ T: 0.017682246905524692
329
328
  track: nukes
330
329
  extras:
331
330
  ambiguous_char: N
@@ -333,15 +332,15 @@ states:
333
332
  germline: C
334
333
  name: IGHD6-13_star_01_8
335
334
  transitions:
336
- IGHD6-13_star_01_9: 0.983739837398374
337
- end: 0.016260162601626018
335
+ IGHD6-13_star_01_9: 0.9896103896103896
336
+ end: 0.010389610389610397
338
337
  - !!python/object:python.hmmwriter.State
339
338
  emissions:
340
339
  probs:
341
- A: 0.90041115338425
342
- C: 0.03319628220525
343
- G: 0.03319628220525
344
- T: 0.03319628220525
340
+ A: 0.950984988931
341
+ C: 0.016338337022999996
342
+ G: 0.016338337022999996
343
+ T: 0.016338337022999996
345
344
  track: nukes
346
345
  extras:
347
346
  ambiguous_char: N
@@ -349,15 +348,15 @@ states:
349
348
  germline: A
350
349
  name: IGHD6-13_star_01_9
351
350
  transitions:
352
- IGHD6-13_star_01_10: 0.981029810298103
353
- end: 0.018970189701897
351
+ IGHD6-13_star_01_10: 0.9844155844155844
352
+ end: 0.015584415584415591
354
353
  - !!python/object:python.hmmwriter.State
355
354
  emissions:
356
355
  probs:
357
- A: 0.03319628220525
358
- C: 0.03319628220525
359
- G: 0.90041115338425
360
- T: 0.03319628220525
356
+ A: 0.016338337022999996
357
+ C: 0.016338337022999996
358
+ G: 0.950984988931
359
+ T: 0.016338337022999996
361
360
  track: nukes
362
361
  extras:
363
362
  ambiguous_char: N
@@ -365,15 +364,15 @@ states:
365
364
  germline: G
366
365
  name: IGHD6-13_star_01_10
367
366
  transitions:
368
- IGHD6-13_star_01_11: 0.962059620596206
369
- end: 0.03794037940379402
367
+ IGHD6-13_star_01_11: 0.9792207792207792
368
+ end: 0.020779220779220786
370
369
  - !!python/object:python.hmmwriter.State
371
370
  emissions:
372
371
  probs:
373
- A: 0.03319628220525
374
- C: 0.90041115338425
375
- G: 0.03319628220525
376
- T: 0.03319628220525
372
+ A: 0.016338337022999996
373
+ C: 0.950984988931
374
+ G: 0.016338337022999996
375
+ T: 0.016338337022999996
377
376
  track: nukes
378
377
  extras:
379
378
  ambiguous_char: N
@@ -381,15 +380,15 @@ states:
381
380
  germline: C
382
381
  name: IGHD6-13_star_01_11
383
382
  transitions:
384
- IGHD6-13_star_01_12: 0.943089430894309
385
- end: 0.05691056910569105
383
+ IGHD6-13_star_01_12: 0.974025974025974
384
+ end: 0.02597402597402598
386
385
  - !!python/object:python.hmmwriter.State
387
386
  emissions:
388
387
  probs:
389
- A: 0.8994883177357544
390
- C: 0.03350389408808183
391
- G: 0.03350389408808183
392
- T: 0.03350389408808183
388
+ A: 0.9478288049998704
389
+ C: 0.017390398333376536
390
+ G: 0.017390398333376536
391
+ T: 0.017390398333376536
393
392
  track: nukes
394
393
  extras:
395
394
  ambiguous_char: N
@@ -397,15 +396,15 @@ states:
397
396
  germline: A
398
397
  name: IGHD6-13_star_01_12
399
398
  transitions:
400
- IGHD6-13_star_01_13: 0.924119241192412
401
- end: 0.07588075880758807
399
+ IGHD6-13_star_01_13: 0.9688311688311688
400
+ end: 0.031168831168831172
402
401
  - !!python/object:python.hmmwriter.State
403
402
  emissions:
404
403
  probs:
405
- A: 0.03381150597091367
406
- C: 0.03381150597091367
407
- G: 0.898565482087259
408
- T: 0.03381150597091367
404
+ A: 0.01844245964375308
405
+ C: 0.01844245964375308
406
+ G: 0.9446726210687407
407
+ T: 0.01844245964375308
409
408
  track: nukes
410
409
  extras:
411
410
  ambiguous_char: N
@@ -413,15 +412,15 @@ states:
413
412
  germline: G
414
413
  name: IGHD6-13_star_01_13
415
414
  transitions:
416
- IGHD6-13_star_01_14: 0.9051490514905149
417
- end: 0.0948509485094851
415
+ IGHD6-13_star_01_14: 0.9636363636363636
416
+ end: 0.03636363636363636
418
417
  - !!python/object:python.hmmwriter.State
419
418
  emissions:
420
419
  probs:
421
- A: 0.034119117853745495
422
- C: 0.8976426464387635
423
- G: 0.034119117853745495
424
- T: 0.034119117853745495
420
+ A: 0.02041682579268518
421
+ C: 0.9387495226219444
422
+ G: 0.02041682579268518
423
+ T: 0.02041682579268518
425
424
  track: nukes
426
425
  extras:
427
426
  ambiguous_char: N
@@ -429,15 +428,15 @@ states:
429
428
  germline: C
430
429
  name: IGHD6-13_star_01_14
431
430
  transitions:
432
- IGHD6-13_star_01_15: 0.8861788617886179
433
- end: 0.11382113821138212
431
+ IGHD6-13_star_01_15: 0.8
432
+ end: 0.2
434
433
  - !!python/object:python.hmmwriter.State
435
434
  emissions:
436
435
  probs:
437
- A: 0.037563954001123626
438
- C: 0.037563954001123626
439
- G: 0.037563954001123626
440
- T: 0.8873081379966291
436
+ A: 0.02991210736575617
437
+ C: 0.02991210736575617
438
+ G: 0.02991210736575617
439
+ T: 0.9102636779027315
441
440
  track: nukes
442
441
  extras:
443
442
  ambiguous_char: N
@@ -445,15 +444,15 @@ states:
445
444
  germline: T
446
445
  name: IGHD6-13_star_01_15
447
446
  transitions:
448
- IGHD6-13_star_01_16: 0.8970189701897019
449
- end: 0.10298102981029811
447
+ IGHD6-13_star_01_16: 0.8727272727272728
448
+ end: 0.12727272727272726
450
449
  - !!python/object:python.hmmwriter.State
451
450
  emissions:
452
451
  probs:
453
- A: 0.0372441210310462
454
- C: 0.0372441210310462
455
- G: 0.8882676369068614
456
- T: 0.0372441210310462
452
+ A: 0.03160084306751974
453
+ C: 0.03160084306751974
454
+ G: 0.9051974707974407
455
+ T: 0.03160084306751974
457
456
  track: nukes
458
457
  extras:
459
458
  ambiguous_char: N
@@ -461,15 +460,15 @@ states:
461
460
  germline: G
462
461
  name: IGHD6-13_star_01_16
463
462
  transitions:
464
- IGHD6-13_star_01_17: 0.9078590785907859
465
- end: 0.09214092140921411
463
+ IGHD6-13_star_01_17: 0.8872727272727272
464
+ end: 0.11272727272727273
466
465
  - !!python/object:python.hmmwriter.State
467
466
  emissions:
468
467
  probs:
469
- A: 0.03692428806096878
470
- C: 0.03692428806096878
471
- G: 0.8892271358170937
472
- T: 0.03692428806096878
468
+ A: 0.030152354504737026
469
+ C: 0.030152354504737026
470
+ G: 0.9095429364857889
471
+ T: 0.030152354504737026
473
472
  track: nukes
474
473
  extras:
475
474
  ambiguous_char: N
@@ -477,15 +476,15 @@ states:
477
476
  germline: G
478
477
  name: IGHD6-13_star_01_17
479
478
  transitions:
480
- IGHD6-13_star_01_18: 0.9186991869918699
481
- end: 0.0813008130081301
479
+ IGHD6-13_star_01_18: 0.9018181818181819
480
+ end: 0.09818181818181819
482
481
  - !!python/object:python.hmmwriter.State
483
482
  emissions:
484
483
  probs:
485
- A: 0.03660445509089136
486
- C: 0.03660445509089136
487
- G: 0.03660445509089136
488
- T: 0.890186634727326
484
+ A: 0.028703865941954308
485
+ C: 0.028703865941954308
486
+ G: 0.028703865941954308
487
+ T: 0.913888402174137
489
488
  track: nukes
490
489
  extras:
491
490
  ambiguous_char: N
@@ -493,15 +492,15 @@ states:
493
492
  germline: T
494
493
  name: IGHD6-13_star_01_18
495
494
  transitions:
496
- IGHD6-13_star_01_19: 0.9295392953929539
497
- end: 0.07046070460704608
495
+ IGHD6-13_star_01_19: 0.9163636363636364
496
+ end: 0.08363636363636363
498
497
  - !!python/object:python.hmmwriter.State
499
498
  emissions:
500
499
  probs:
501
- A: 0.8911461336375582
502
- C: 0.03628462212081393
503
- G: 0.03628462212081393
504
- T: 0.03628462212081393
500
+ A: 0.9182338678624852
501
+ C: 0.027255377379171598
502
+ G: 0.027255377379171598
503
+ T: 0.027255377379171598
505
504
  track: nukes
506
505
  extras:
507
506
  ambiguous_char: N
@@ -509,15 +508,15 @@ states:
509
508
  germline: A
510
509
  name: IGHD6-13_star_01_19
511
510
  transitions:
512
- IGHD6-13_star_01_20: 0.940379403794038
513
- end: 0.05962059620596207
511
+ IGHD6-13_star_01_20: 0.9309090909090909
512
+ end: 0.06909090909090909
514
513
  - !!python/object:python.hmmwriter.State
515
514
  emissions:
516
515
  probs:
517
- A: 0.035964789150736504
518
- C: 0.8921056325477905
519
- G: 0.035964789150736504
520
- T: 0.035964789150736504
516
+ A: 0.02580688881638888
517
+ C: 0.9225793335508333
518
+ G: 0.02580688881638888
519
+ T: 0.02580688881638888
521
520
  track: nukes
522
521
  extras:
523
522
  ambiguous_char: N