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/simu/hmm/hmms/IGHJ6_star_02.yaml CHANGED
@@ -1,8 +1,8 @@
1
1
  !!python/object:python.hmmwriter.HMM
2
2
  extras:
3
- gene_prob: 0.3
4
- overall_mute_freq: 0.019000000000000003
5
- per_gene_mute_freq: 0.1123625967300556
3
+ gene_prob: 0.08333333333333333
4
+ overall_mute_freq: 0.012499999999999999
5
+ per_gene_mute_freq: 0.11268189142795679
6
6
  name: IGHJ6_star_02
7
7
  states:
8
8
  - !!python/object:python.hmmwriter.State
@@ -10,47 +10,47 @@ states:
10
10
  extras: {}
11
11
  name: init
12
12
  transitions:
13
- IGHJ6_star_02_0: 0.005919220055710305
14
- IGHJ6_star_02_1: 0.005919220055710305
15
- IGHJ6_star_02_10: 0.005919220055710305
16
- IGHJ6_star_02_11: 0.005919220055710305
17
- IGHJ6_star_02_12: 0.005919220055710305
18
- IGHJ6_star_02_13: 0.005919220055710305
19
- IGHJ6_star_02_14: 0.005919220055710305
20
- IGHJ6_star_02_15: 0.005919220055710305
21
- IGHJ6_star_02_16: 0.005919220055710305
22
- IGHJ6_star_02_17: 0.017757660167130915
23
- IGHJ6_star_02_18: 0.01671309192200557
24
- IGHJ6_star_02_19: 0.01566852367688022
25
- IGHJ6_star_02_2: 0.005919220055710305
26
- IGHJ6_star_02_20: 0.014623955431754872
27
- IGHJ6_star_02_21: 0.013579387186629526
28
- IGHJ6_star_02_22: 0.01253481894150418
29
- IGHJ6_star_02_23: 0.011490250696378832
30
- IGHJ6_star_02_24: 0.010445682451253484
31
- IGHJ6_star_02_25: 0.009401114206128136
32
- IGHJ6_star_02_26: 0.008356545961002788
33
- IGHJ6_star_02_27: 0.00731197771587744
34
- IGHJ6_star_02_28: 0.006267409470752091
35
- IGHJ6_star_02_29: 0.005222841225626743
36
- IGHJ6_star_02_3: 0.005919220055710305
37
- IGHJ6_star_02_4: 0.005919220055710305
38
- IGHJ6_star_02_5: 0.005919220055710305
39
- IGHJ6_star_02_6: 0.005919220055710305
40
- IGHJ6_star_02_7: 0.005919220055710305
41
- IGHJ6_star_02_8: 0.005919220055710305
42
- IGHJ6_star_02_9: 0.005919220055710305
43
- insert_left_A: 0.12890625
44
- insert_left_C: 0.1875
45
- insert_left_G: 0.1875
46
- insert_left_T: 0.24609375
47
- - !!python/object:python.hmmwriter.State
48
- emissions:
49
- probs:
50
- A: 0.8876374032699444
51
- C: 0.037454198910018534
52
- G: 0.037454198910018534
53
- T: 0.037454198910018534
13
+ IGHJ6_star_02_0: 0.005297187816468022
14
+ IGHJ6_star_02_1: 0.005297187816468022
15
+ IGHJ6_star_02_10: 0.005297187816468022
16
+ IGHJ6_star_02_11: 0.005297187816468022
17
+ IGHJ6_star_02_12: 0.005297187816468022
18
+ IGHJ6_star_02_13: 0.005297187816468022
19
+ IGHJ6_star_02_14: 0.005297187816468022
20
+ IGHJ6_star_02_15: 0.005297187816468022
21
+ IGHJ6_star_02_16: 0.007945781724702032
22
+ IGHJ6_star_02_17: 0.010594375632936043
23
+ IGHJ6_star_02_18: 0.009971177066292747
24
+ IGHJ6_star_02_19: 0.00934797849964945
25
+ IGHJ6_star_02_2: 0.005297187816468022
26
+ IGHJ6_star_02_20: 0.008724779933006153
27
+ IGHJ6_star_02_21: 0.008101581366362857
28
+ IGHJ6_star_02_22: 0.007478382799719559
29
+ IGHJ6_star_02_23: 0.006855184233076262
30
+ IGHJ6_star_02_24: 0.006231985666432965
31
+ IGHJ6_star_02_25: 0.005608787099789668
32
+ IGHJ6_star_02_26: 0.0049855885331463725
33
+ IGHJ6_star_02_27: 0.004362389966503075
34
+ IGHJ6_star_02_28: 0.0037391913998597783
35
+ IGHJ6_star_02_29: 0.003115992833216482
36
+ IGHJ6_star_02_3: 0.005297187816468022
37
+ IGHJ6_star_02_4: 0.005297187816468022
38
+ IGHJ6_star_02_5: 0.005297187816468022
39
+ IGHJ6_star_02_6: 0.005297187816468022
40
+ IGHJ6_star_02_7: 0.005297187816468022
41
+ IGHJ6_star_02_8: 0.005297187816468022
42
+ IGHJ6_star_02_9: 0.005297187816468022
43
+ insert_left_A: 0.09935064935064934
44
+ insert_left_C: 0.3331168831168831
45
+ insert_left_G: 0.12857142857142856
46
+ insert_left_T: 0.2571428571428571
47
+ - !!python/object:python.hmmwriter.State
48
+ emissions:
49
+ probs:
50
+ A: 0.8873181085720432
51
+ C: 0.037560630475985596
52
+ G: 0.037560630475985596
53
+ T: 0.037560630475985596
54
54
  track: nukes
55
55
  extras:
56
56
  ambiguous_char: N
@@ -58,47 +58,47 @@ states:
58
58
  germline: A
59
59
  name: insert_left_A
60
60
  transitions:
61
- IGHJ6_star_02_0: 0.0016615354542344714
62
- IGHJ6_star_02_1: 0.0016615354542344714
63
- IGHJ6_star_02_10: 0.0016615354542344714
64
- IGHJ6_star_02_11: 0.0016615354542344714
65
- IGHJ6_star_02_12: 0.0016615354542344714
66
- IGHJ6_star_02_13: 0.0016615354542344714
67
- IGHJ6_star_02_14: 0.0016615354542344714
68
- IGHJ6_star_02_15: 0.0016615354542344714
69
- IGHJ6_star_02_16: 0.0016615354542344714
70
- IGHJ6_star_02_17: 0.004984606362703414
71
- IGHJ6_star_02_18: 0.004691394223720861
72
- IGHJ6_star_02_19: 0.004398182084738307
73
- IGHJ6_star_02_2: 0.0016615354542344714
74
- IGHJ6_star_02_20: 0.004104969945755753
75
- IGHJ6_star_02_21: 0.0038117578067732
76
- IGHJ6_star_02_22: 0.0035185456677906467
77
- IGHJ6_star_02_23: 0.003225333528808093
78
- IGHJ6_star_02_24: 0.0029321213898255392
79
- IGHJ6_star_02_25: 0.0026389092508429853
80
- IGHJ6_star_02_26: 0.0023456971118604314
81
- IGHJ6_star_02_27: 0.002052484972877878
82
- IGHJ6_star_02_28: 0.0017592728338953235
83
- IGHJ6_star_02_29: 0.0014660606949127698
84
- IGHJ6_star_02_3: 0.0016615354542344714
85
- IGHJ6_star_02_4: 0.0016615354542344714
86
- IGHJ6_star_02_5: 0.0016615354542344714
87
- IGHJ6_star_02_6: 0.0016615354542344714
88
- IGHJ6_star_02_7: 0.0016615354542344714
89
- IGHJ6_star_02_8: 0.0016615354542344714
90
- IGHJ6_star_02_9: 0.0016615354542344714
91
- insert_left_A: 0.15981359649122806
92
- insert_left_C: 0.2324561403508772
93
- insert_left_G: 0.2324561403508772
94
- insert_left_T: 0.3050986842105263
95
- - !!python/object:python.hmmwriter.State
96
- emissions:
97
- probs:
98
- A: 0.037454198910018534
99
- C: 0.8876374032699444
100
- G: 0.037454198910018534
101
- T: 0.037454198910018534
61
+ IGHJ6_star_02_0: 0.001954145505465339
62
+ IGHJ6_star_02_1: 0.001954145505465339
63
+ IGHJ6_star_02_10: 0.001954145505465339
64
+ IGHJ6_star_02_11: 0.001954145505465339
65
+ IGHJ6_star_02_12: 0.001954145505465339
66
+ IGHJ6_star_02_13: 0.001954145505465339
67
+ IGHJ6_star_02_14: 0.001954145505465339
68
+ IGHJ6_star_02_15: 0.001954145505465339
69
+ IGHJ6_star_02_16: 0.0029312182581980083
70
+ IGHJ6_star_02_17: 0.003908291010930678
71
+ IGHJ6_star_02_18: 0.003678391539699462
72
+ IGHJ6_star_02_19: 0.003448492068468245
73
+ IGHJ6_star_02_2: 0.001954145505465339
74
+ IGHJ6_star_02_20: 0.0032185925972370286
75
+ IGHJ6_star_02_21: 0.0029886931260058123
76
+ IGHJ6_star_02_22: 0.002758793654774596
77
+ IGHJ6_star_02_23: 0.002528894183543379
78
+ IGHJ6_star_02_24: 0.0022989947123121628
79
+ IGHJ6_star_02_25: 0.002069095241080947
80
+ IGHJ6_star_02_26: 0.0018391957698497305
81
+ IGHJ6_star_02_27: 0.0016092962986185139
82
+ IGHJ6_star_02_28: 0.0013793968273872975
83
+ IGHJ6_star_02_29: 0.0011494973561560812
84
+ IGHJ6_star_02_3: 0.001954145505465339
85
+ IGHJ6_star_02_4: 0.001954145505465339
86
+ IGHJ6_star_02_5: 0.001954145505465339
87
+ IGHJ6_star_02_6: 0.001954145505465339
88
+ IGHJ6_star_02_7: 0.001954145505465339
89
+ IGHJ6_star_02_8: 0.001954145505465339
90
+ IGHJ6_star_02_9: 0.001954145505465339
91
+ insert_left_A: 0.11328397212543553
92
+ insert_left_C: 0.37983449477351916
93
+ insert_left_G: 0.14660278745644598
94
+ insert_left_T: 0.29320557491289195
95
+ - !!python/object:python.hmmwriter.State
96
+ emissions:
97
+ probs:
98
+ A: 0.037560630475985596
99
+ C: 0.8873181085720432
100
+ G: 0.037560630475985596
101
+ T: 0.037560630475985596
102
102
  track: nukes
103
103
  extras:
104
104
  ambiguous_char: N
@@ -106,47 +106,47 @@ states:
106
106
  germline: C
107
107
  name: insert_left_C
108
108
  transitions:
109
- IGHJ6_star_02_0: 0.0016615354542344714
110
- IGHJ6_star_02_1: 0.0016615354542344714
111
- IGHJ6_star_02_10: 0.0016615354542344714
112
- IGHJ6_star_02_11: 0.0016615354542344714
113
- IGHJ6_star_02_12: 0.0016615354542344714
114
- IGHJ6_star_02_13: 0.0016615354542344714
115
- IGHJ6_star_02_14: 0.0016615354542344714
116
- IGHJ6_star_02_15: 0.0016615354542344714
117
- IGHJ6_star_02_16: 0.0016615354542344714
118
- IGHJ6_star_02_17: 0.004984606362703414
119
- IGHJ6_star_02_18: 0.004691394223720861
120
- IGHJ6_star_02_19: 0.004398182084738307
121
- IGHJ6_star_02_2: 0.0016615354542344714
122
- IGHJ6_star_02_20: 0.004104969945755753
123
- IGHJ6_star_02_21: 0.0038117578067732
124
- IGHJ6_star_02_22: 0.0035185456677906467
125
- IGHJ6_star_02_23: 0.003225333528808093
126
- IGHJ6_star_02_24: 0.0029321213898255392
127
- IGHJ6_star_02_25: 0.0026389092508429853
128
- IGHJ6_star_02_26: 0.0023456971118604314
129
- IGHJ6_star_02_27: 0.002052484972877878
130
- IGHJ6_star_02_28: 0.0017592728338953235
131
- IGHJ6_star_02_29: 0.0014660606949127698
132
- IGHJ6_star_02_3: 0.0016615354542344714
133
- IGHJ6_star_02_4: 0.0016615354542344714
134
- IGHJ6_star_02_5: 0.0016615354542344714
135
- IGHJ6_star_02_6: 0.0016615354542344714
136
- IGHJ6_star_02_7: 0.0016615354542344714
137
- IGHJ6_star_02_8: 0.0016615354542344714
138
- IGHJ6_star_02_9: 0.0016615354542344714
139
- insert_left_A: 0.15981359649122806
140
- insert_left_C: 0.2324561403508772
141
- insert_left_G: 0.2324561403508772
142
- insert_left_T: 0.3050986842105263
143
- - !!python/object:python.hmmwriter.State
144
- emissions:
145
- probs:
146
- A: 0.037454198910018534
147
- C: 0.037454198910018534
148
- G: 0.8876374032699444
149
- T: 0.037454198910018534
109
+ IGHJ6_star_02_0: 0.001954145505465339
110
+ IGHJ6_star_02_1: 0.001954145505465339
111
+ IGHJ6_star_02_10: 0.001954145505465339
112
+ IGHJ6_star_02_11: 0.001954145505465339
113
+ IGHJ6_star_02_12: 0.001954145505465339
114
+ IGHJ6_star_02_13: 0.001954145505465339
115
+ IGHJ6_star_02_14: 0.001954145505465339
116
+ IGHJ6_star_02_15: 0.001954145505465339
117
+ IGHJ6_star_02_16: 0.0029312182581980083
118
+ IGHJ6_star_02_17: 0.003908291010930678
119
+ IGHJ6_star_02_18: 0.003678391539699462
120
+ IGHJ6_star_02_19: 0.003448492068468245
121
+ IGHJ6_star_02_2: 0.001954145505465339
122
+ IGHJ6_star_02_20: 0.0032185925972370286
123
+ IGHJ6_star_02_21: 0.0029886931260058123
124
+ IGHJ6_star_02_22: 0.002758793654774596
125
+ IGHJ6_star_02_23: 0.002528894183543379
126
+ IGHJ6_star_02_24: 0.0022989947123121628
127
+ IGHJ6_star_02_25: 0.002069095241080947
128
+ IGHJ6_star_02_26: 0.0018391957698497305
129
+ IGHJ6_star_02_27: 0.0016092962986185139
130
+ IGHJ6_star_02_28: 0.0013793968273872975
131
+ IGHJ6_star_02_29: 0.0011494973561560812
132
+ IGHJ6_star_02_3: 0.001954145505465339
133
+ IGHJ6_star_02_4: 0.001954145505465339
134
+ IGHJ6_star_02_5: 0.001954145505465339
135
+ IGHJ6_star_02_6: 0.001954145505465339
136
+ IGHJ6_star_02_7: 0.001954145505465339
137
+ IGHJ6_star_02_8: 0.001954145505465339
138
+ IGHJ6_star_02_9: 0.001954145505465339
139
+ insert_left_A: 0.11328397212543553
140
+ insert_left_C: 0.37983449477351916
141
+ insert_left_G: 0.14660278745644598
142
+ insert_left_T: 0.29320557491289195
143
+ - !!python/object:python.hmmwriter.State
144
+ emissions:
145
+ probs:
146
+ A: 0.037560630475985596
147
+ C: 0.037560630475985596
148
+ G: 0.8873181085720432
149
+ T: 0.037560630475985596
150
150
  track: nukes
151
151
  extras:
152
152
  ambiguous_char: N
@@ -154,47 +154,47 @@ states:
154
154
  germline: G
155
155
  name: insert_left_G
156
156
  transitions:
157
- IGHJ6_star_02_0: 0.0016615354542344714
158
- IGHJ6_star_02_1: 0.0016615354542344714
159
- IGHJ6_star_02_10: 0.0016615354542344714
160
- IGHJ6_star_02_11: 0.0016615354542344714
161
- IGHJ6_star_02_12: 0.0016615354542344714
162
- IGHJ6_star_02_13: 0.0016615354542344714
163
- IGHJ6_star_02_14: 0.0016615354542344714
164
- IGHJ6_star_02_15: 0.0016615354542344714
165
- IGHJ6_star_02_16: 0.0016615354542344714
166
- IGHJ6_star_02_17: 0.004984606362703414
167
- IGHJ6_star_02_18: 0.004691394223720861
168
- IGHJ6_star_02_19: 0.004398182084738307
169
- IGHJ6_star_02_2: 0.0016615354542344714
170
- IGHJ6_star_02_20: 0.004104969945755753
171
- IGHJ6_star_02_21: 0.0038117578067732
172
- IGHJ6_star_02_22: 0.0035185456677906467
173
- IGHJ6_star_02_23: 0.003225333528808093
174
- IGHJ6_star_02_24: 0.0029321213898255392
175
- IGHJ6_star_02_25: 0.0026389092508429853
176
- IGHJ6_star_02_26: 0.0023456971118604314
177
- IGHJ6_star_02_27: 0.002052484972877878
178
- IGHJ6_star_02_28: 0.0017592728338953235
179
- IGHJ6_star_02_29: 0.0014660606949127698
180
- IGHJ6_star_02_3: 0.0016615354542344714
181
- IGHJ6_star_02_4: 0.0016615354542344714
182
- IGHJ6_star_02_5: 0.0016615354542344714
183
- IGHJ6_star_02_6: 0.0016615354542344714
184
- IGHJ6_star_02_7: 0.0016615354542344714
185
- IGHJ6_star_02_8: 0.0016615354542344714
186
- IGHJ6_star_02_9: 0.0016615354542344714
187
- insert_left_A: 0.15981359649122806
188
- insert_left_C: 0.2324561403508772
189
- insert_left_G: 0.2324561403508772
190
- insert_left_T: 0.3050986842105263
191
- - !!python/object:python.hmmwriter.State
192
- emissions:
193
- probs:
194
- A: 0.037454198910018534
195
- C: 0.037454198910018534
196
- G: 0.037454198910018534
197
- T: 0.8876374032699444
157
+ IGHJ6_star_02_0: 0.001954145505465339
158
+ IGHJ6_star_02_1: 0.001954145505465339
159
+ IGHJ6_star_02_10: 0.001954145505465339
160
+ IGHJ6_star_02_11: 0.001954145505465339
161
+ IGHJ6_star_02_12: 0.001954145505465339
162
+ IGHJ6_star_02_13: 0.001954145505465339
163
+ IGHJ6_star_02_14: 0.001954145505465339
164
+ IGHJ6_star_02_15: 0.001954145505465339
165
+ IGHJ6_star_02_16: 0.0029312182581980083
166
+ IGHJ6_star_02_17: 0.003908291010930678
167
+ IGHJ6_star_02_18: 0.003678391539699462
168
+ IGHJ6_star_02_19: 0.003448492068468245
169
+ IGHJ6_star_02_2: 0.001954145505465339
170
+ IGHJ6_star_02_20: 0.0032185925972370286
171
+ IGHJ6_star_02_21: 0.0029886931260058123
172
+ IGHJ6_star_02_22: 0.002758793654774596
173
+ IGHJ6_star_02_23: 0.002528894183543379
174
+ IGHJ6_star_02_24: 0.0022989947123121628
175
+ IGHJ6_star_02_25: 0.002069095241080947
176
+ IGHJ6_star_02_26: 0.0018391957698497305
177
+ IGHJ6_star_02_27: 0.0016092962986185139
178
+ IGHJ6_star_02_28: 0.0013793968273872975
179
+ IGHJ6_star_02_29: 0.0011494973561560812
180
+ IGHJ6_star_02_3: 0.001954145505465339
181
+ IGHJ6_star_02_4: 0.001954145505465339
182
+ IGHJ6_star_02_5: 0.001954145505465339
183
+ IGHJ6_star_02_6: 0.001954145505465339
184
+ IGHJ6_star_02_7: 0.001954145505465339
185
+ IGHJ6_star_02_8: 0.001954145505465339
186
+ IGHJ6_star_02_9: 0.001954145505465339
187
+ insert_left_A: 0.11328397212543553
188
+ insert_left_C: 0.37983449477351916
189
+ insert_left_G: 0.14660278745644598
190
+ insert_left_T: 0.29320557491289195
191
+ - !!python/object:python.hmmwriter.State
192
+ emissions:
193
+ probs:
194
+ A: 0.037560630475985596
195
+ C: 0.037560630475985596
196
+ G: 0.037560630475985596
197
+ T: 0.8873181085720432
198
198
  track: nukes
199
199
  extras:
200
200
  ambiguous_char: N
@@ -202,47 +202,47 @@ states:
202
202
  germline: T
203
203
  name: insert_left_T
204
204
  transitions:
205
- IGHJ6_star_02_0: 0.0016615354542344714
206
- IGHJ6_star_02_1: 0.0016615354542344714
207
- IGHJ6_star_02_10: 0.0016615354542344714
208
- IGHJ6_star_02_11: 0.0016615354542344714
209
- IGHJ6_star_02_12: 0.0016615354542344714
210
- IGHJ6_star_02_13: 0.0016615354542344714
211
- IGHJ6_star_02_14: 0.0016615354542344714
212
- IGHJ6_star_02_15: 0.0016615354542344714
213
- IGHJ6_star_02_16: 0.0016615354542344714
214
- IGHJ6_star_02_17: 0.004984606362703414
215
- IGHJ6_star_02_18: 0.004691394223720861
216
- IGHJ6_star_02_19: 0.004398182084738307
217
- IGHJ6_star_02_2: 0.0016615354542344714
218
- IGHJ6_star_02_20: 0.004104969945755753
219
- IGHJ6_star_02_21: 0.0038117578067732
220
- IGHJ6_star_02_22: 0.0035185456677906467
221
- IGHJ6_star_02_23: 0.003225333528808093
222
- IGHJ6_star_02_24: 0.0029321213898255392
223
- IGHJ6_star_02_25: 0.0026389092508429853
224
- IGHJ6_star_02_26: 0.0023456971118604314
225
- IGHJ6_star_02_27: 0.002052484972877878
226
- IGHJ6_star_02_28: 0.0017592728338953235
227
- IGHJ6_star_02_29: 0.0014660606949127698
228
- IGHJ6_star_02_3: 0.0016615354542344714
229
- IGHJ6_star_02_4: 0.0016615354542344714
230
- IGHJ6_star_02_5: 0.0016615354542344714
231
- IGHJ6_star_02_6: 0.0016615354542344714
232
- IGHJ6_star_02_7: 0.0016615354542344714
233
- IGHJ6_star_02_8: 0.0016615354542344714
234
- IGHJ6_star_02_9: 0.0016615354542344714
235
- insert_left_A: 0.15981359649122806
236
- insert_left_C: 0.2324561403508772
237
- insert_left_G: 0.2324561403508772
238
- insert_left_T: 0.3050986842105263
239
- - !!python/object:python.hmmwriter.State
240
- emissions:
241
- probs:
242
- A: 0.8876374032699444
243
- C: 0.03745419891001853
244
- G: 0.03745419891001853
245
- T: 0.03745419891001853
205
+ IGHJ6_star_02_0: 0.001954145505465339
206
+ IGHJ6_star_02_1: 0.001954145505465339
207
+ IGHJ6_star_02_10: 0.001954145505465339
208
+ IGHJ6_star_02_11: 0.001954145505465339
209
+ IGHJ6_star_02_12: 0.001954145505465339
210
+ IGHJ6_star_02_13: 0.001954145505465339
211
+ IGHJ6_star_02_14: 0.001954145505465339
212
+ IGHJ6_star_02_15: 0.001954145505465339
213
+ IGHJ6_star_02_16: 0.0029312182581980083
214
+ IGHJ6_star_02_17: 0.003908291010930678
215
+ IGHJ6_star_02_18: 0.003678391539699462
216
+ IGHJ6_star_02_19: 0.003448492068468245
217
+ IGHJ6_star_02_2: 0.001954145505465339
218
+ IGHJ6_star_02_20: 0.0032185925972370286
219
+ IGHJ6_star_02_21: 0.0029886931260058123
220
+ IGHJ6_star_02_22: 0.002758793654774596
221
+ IGHJ6_star_02_23: 0.002528894183543379
222
+ IGHJ6_star_02_24: 0.0022989947123121628
223
+ IGHJ6_star_02_25: 0.002069095241080947
224
+ IGHJ6_star_02_26: 0.0018391957698497305
225
+ IGHJ6_star_02_27: 0.0016092962986185139
226
+ IGHJ6_star_02_28: 0.0013793968273872975
227
+ IGHJ6_star_02_29: 0.0011494973561560812
228
+ IGHJ6_star_02_3: 0.001954145505465339
229
+ IGHJ6_star_02_4: 0.001954145505465339
230
+ IGHJ6_star_02_5: 0.001954145505465339
231
+ IGHJ6_star_02_6: 0.001954145505465339
232
+ IGHJ6_star_02_7: 0.001954145505465339
233
+ IGHJ6_star_02_8: 0.001954145505465339
234
+ IGHJ6_star_02_9: 0.001954145505465339
235
+ insert_left_A: 0.11328397212543553
236
+ insert_left_C: 0.37983449477351916
237
+ insert_left_G: 0.14660278745644598
238
+ insert_left_T: 0.29320557491289195
239
+ - !!python/object:python.hmmwriter.State
240
+ emissions:
241
+ probs:
242
+ A: 0.8873181085720432
243
+ C: 0.037560630475985596
244
+ G: 0.037560630475985596
245
+ T: 0.037560630475985596
246
246
  track: nukes
247
247
  extras:
248
248
  ambiguous_char: N
@@ -254,10 +254,10 @@ states:
254
254
  - !!python/object:python.hmmwriter.State
255
255
  emissions:
256
256
  probs:
257
- A: 0.03724815563118427
258
- C: 0.03724815563118427
259
- G: 0.03724815563118427
260
- T: 0.8882555331064472
257
+ A: 0.037349265618852975
258
+ C: 0.037349265618852975
259
+ G: 0.037349265618852975
260
+ T: 0.887952203143441
261
261
  track: nukes
262
262
  extras:
263
263
  ambiguous_char: N
@@ -269,10 +269,10 @@ states:
269
269
  - !!python/object:python.hmmwriter.State
270
270
  emissions:
271
271
  probs:
272
- A: 0.03704211235235001
273
- C: 0.03704211235235001
274
- G: 0.03704211235235001
275
- T: 0.88887366294295
272
+ A: 0.03713790076172037
273
+ C: 0.03713790076172037
274
+ G: 0.03713790076172037
275
+ T: 0.8885862977148389
276
276
  track: nukes
277
277
  extras:
278
278
  ambiguous_char: N
@@ -284,10 +284,10 @@ states:
284
284
  - !!python/object:python.hmmwriter.State
285
285
  emissions:
286
286
  probs:
287
- A: 0.8894917927794528
288
- C: 0.03683606907351575
289
- G: 0.03683606907351575
290
- T: 0.03683606907351575
287
+ A: 0.8892203922862367
288
+ C: 0.036926535904587755
289
+ G: 0.036926535904587755
290
+ T: 0.036926535904587755
291
291
  track: nukes
292
292
  extras:
293
293
  ambiguous_char: N
@@ -299,10 +299,10 @@ states:
299
299
  - !!python/object:python.hmmwriter.State
300
300
  emissions:
301
301
  probs:
302
- A: 0.03663002579468149
303
- C: 0.8901099226159556
304
- G: 0.03663002579468149
305
- T: 0.03663002579468149
302
+ A: 0.03671517104745514
303
+ C: 0.8898544868576346
304
+ G: 0.03671517104745514
305
+ T: 0.03671517104745514
306
306
  track: nukes
307
307
  extras:
308
308
  ambiguous_char: N
@@ -314,10 +314,10 @@ states:
314
314
  - !!python/object:python.hmmwriter.State
315
315
  emissions:
316
316
  probs:
317
- A: 0.036423982515847234
318
- C: 0.036423982515847234
319
- G: 0.036423982515847234
320
- T: 0.8907280524524583
317
+ A: 0.03650380619032252
318
+ C: 0.03650380619032252
319
+ G: 0.03650380619032252
320
+ T: 0.8904885814290324
321
321
  track: nukes
322
322
  extras:
323
323
  ambiguous_char: N
@@ -329,10 +329,10 @@ states:
329
329
  - !!python/object:python.hmmwriter.State
330
330
  emissions:
331
331
  probs:
332
- A: 0.8913461822889611
333
- C: 0.03621793923701297
334
- G: 0.03621793923701297
335
- T: 0.03621793923701297
332
+ A: 0.8911226760004303
333
+ C: 0.036292441333189915
334
+ G: 0.036292441333189915
335
+ T: 0.036292441333189915
336
336
  track: nukes
337
337
  extras:
338
338
  ambiguous_char: N
@@ -344,10 +344,10 @@ states:
344
344
  - !!python/object:python.hmmwriter.State
345
345
  emissions:
346
346
  probs:
347
- A: 0.03601189595817871
348
- C: 0.8919643121254639
349
- G: 0.03601189595817871
350
- T: 0.03601189595817871
347
+ A: 0.0360810764760573
348
+ C: 0.8917567705718281
349
+ G: 0.0360810764760573
350
+ T: 0.0360810764760573
351
351
  track: nukes
352
352
  extras:
353
353
  ambiguous_char: N
@@ -359,10 +359,10 @@ states:
359
359
  - !!python/object:python.hmmwriter.State
360
360
  emissions:
361
361
  probs:
362
- A: 0.03580585267934445
363
- C: 0.03580585267934445
364
- G: 0.03580585267934445
365
- T: 0.8925824419619667
362
+ A: 0.03586971161892469
363
+ C: 0.03586971161892469
364
+ G: 0.03586971161892469
365
+ T: 0.892390865143226
366
366
  track: nukes
367
367
  extras:
368
368
  ambiguous_char: N
@@ -374,10 +374,10 @@ states:
374
374
  - !!python/object:python.hmmwriter.State
375
375
  emissions:
376
376
  probs:
377
- A: 0.8932005717984695
378
- C: 0.03559980940051019
379
- G: 0.03559980940051019
380
- T: 0.03559980940051019
377
+ A: 0.8930249597146238
378
+ C: 0.035658346761792074
379
+ G: 0.035658346761792074
380
+ T: 0.035658346761792074
381
381
  track: nukes
382
382
  extras:
383
383
  ambiguous_char: N
@@ -389,10 +389,10 @@ states:
389
389
  - !!python/object:python.hmmwriter.State
390
390
  emissions:
391
391
  probs:
392
- A: 0.035393766121675926
393
- C: 0.8938187016349722
394
- G: 0.035393766121675926
395
- T: 0.035393766121675926
392
+ A: 0.03544698190465946
393
+ C: 0.8936590542860217
394
+ G: 0.03544698190465946
395
+ T: 0.03544698190465946
396
396
  track: nukes
397
397
  extras:
398
398
  ambiguous_char: N
@@ -404,10 +404,10 @@ states:
404
404
  - !!python/object:python.hmmwriter.State
405
405
  emissions:
406
406
  probs:
407
- A: 0.035187722842841676
408
- C: 0.035187722842841676
409
- G: 0.035187722842841676
410
- T: 0.894436831471475
407
+ A: 0.035235617047526854
408
+ C: 0.035235617047526854
409
+ G: 0.035235617047526854
410
+ T: 0.8942931488574194
411
411
  track: nukes
412
412
  extras:
413
413
  ambiguous_char: N
@@ -419,10 +419,10 @@ states:
419
419
  - !!python/object:python.hmmwriter.State
420
420
  emissions:
421
421
  probs:
422
- A: 0.8950549613079778
423
- C: 0.03498167956400741
424
- G: 0.03498167956400741
425
- T: 0.03498167956400741
422
+ A: 0.8949272434288172
423
+ C: 0.03502425219039424
424
+ G: 0.03502425219039424
425
+ T: 0.03502425219039424
426
426
  track: nukes
427
427
  extras:
428
428
  ambiguous_char: N
@@ -434,10 +434,10 @@ states:
434
434
  - !!python/object:python.hmmwriter.State
435
435
  emissions:
436
436
  probs:
437
- A: 0.034775636285173155
438
- C: 0.8956730911444806
439
- G: 0.034775636285173155
440
- T: 0.034775636285173155
437
+ A: 0.03481288733326163
438
+ C: 0.8955613380002151
439
+ G: 0.03481288733326163
440
+ T: 0.03481288733326163
441
441
  track: nukes
442
442
  extras:
443
443
  ambiguous_char: N
@@ -449,10 +449,10 @@ states:
449
449
  - !!python/object:python.hmmwriter.State
450
450
  emissions:
451
451
  probs:
452
- A: 0.03456959300633889
453
- C: 0.03456959300633889
454
- G: 0.03456959300633889
455
- T: 0.8962912209809833
452
+ A: 0.03460152247612901
453
+ C: 0.03460152247612901
454
+ G: 0.03460152247612901
455
+ T: 0.8961954325716129
456
456
  track: nukes
457
457
  extras:
458
458
  ambiguous_char: N
@@ -464,10 +464,10 @@ states:
464
464
  - !!python/object:python.hmmwriter.State
465
465
  emissions:
466
466
  probs:
467
- A: 0.8969093508174861
468
- C: 0.03436354972750463
469
- G: 0.03436354972750463
470
- T: 0.03436354972750463
467
+ A: 0.8911178526671796
468
+ C: 0.036294049110940155
469
+ G: 0.036294049110940155
470
+ T: 0.036294049110940155
471
471
  track: nukes
472
472
  extras:
473
473
  ambiguous_char: N
@@ -479,10 +479,10 @@ states:
479
479
  - !!python/object:python.hmmwriter.State
480
480
  emissions:
481
481
  probs:
482
- A: 0.03415750644867037
483
- C: 0.8975274806539889
484
- G: 0.03415750644867037
485
- T: 0.03415750644867037
482
+ A: 0.037512126095197114
483
+ C: 0.8874636217144086
484
+ G: 0.037512126095197114
485
+ T: 0.037512126095197114
486
486
  track: nukes
487
487
  extras:
488
488
  ambiguous_char: N
@@ -494,10 +494,10 @@ states:
494
494
  - !!python/object:python.hmmwriter.State
495
495
  emissions:
496
496
  probs:
497
- A: 0.038634922835721106
498
- C: 0.038634922835721106
499
- G: 0.8840952314928366
500
- T: 0.038634922835721106
497
+ A: 0.03865088757061616
498
+ C: 0.03865088757061616
499
+ G: 0.8840473372881515
500
+ T: 0.03865088757061616
501
501
  track: nukes
502
502
  extras:
503
503
  ambiguous_char: N
@@ -509,10 +509,10 @@ states:
509
509
  - !!python/object:python.hmmwriter.State
510
510
  emissions:
511
511
  probs:
512
- A: 0.038704377184291844
513
- C: 0.038704377184291844
514
- G: 0.8838868684471245
515
- T: 0.038704377184291844
512
+ A: 0.038715020340888556
513
+ C: 0.038715020340888556
514
+ G: 0.8838549389773344
515
+ T: 0.038715020340888556
516
516
  track: nukes
517
517
  extras:
518
518
  ambiguous_char: N
@@ -524,10 +524,10 @@ states:
524
524
  - !!python/object:python.hmmwriter.State
525
525
  emissions:
526
526
  probs:
527
- A: 0.038773831532862596
528
- C: 0.038773831532862596
529
- G: 0.038773831532862596
530
- T: 0.8836785054014122
527
+ A: 0.03877915311116094
528
+ C: 0.03877915311116094
529
+ G: 0.03877915311116094
530
+ T: 0.8836625406665172
531
531
  track: nukes
532
532
  extras:
533
533
  ambiguous_char: N