partis-bcr 1.0.11__cp312-cp312-macosx_10_13_universal2.whl → 1.0.11.post1.dev7__cp312-cp312-macosx_10_13_universal2.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (644) 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.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +644 -126
  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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  632. test/trees.nwk +100 -0
  633. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  634. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  635. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  636. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  637. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  638. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  639. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  640. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  641. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  642. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  643. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  644. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/hmm/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: 0.11166078445944759
3
+ gene_prob: 0.6388888888888888
4
+ overall_mute_freq: 0.012499999999999999
5
+ per_gene_mute_freq: 0.08292763032579839
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: 0.002840909090909091
14
- IGHD6-13_star_01_1: 0.002840909090909091
15
- IGHD6-13_star_01_10: 0.004870129870129871
16
- IGHD6-13_star_01_11: 0.003652597402597404
17
- IGHD6-13_star_01_12: 0.002435064935064936
18
- IGHD6-13_star_01_13: 0.0012175324675324684
19
- IGHD6-13_star_01_14: 9.462128050782583e-19
20
- IGHD6-13_star_01_15: 0.002840909090909091
21
- IGHD6-13_star_01_16: 0.002840909090909091
22
- IGHD6-13_star_01_17: 0.002840909090909091
23
- IGHD6-13_star_01_18: 0.002840909090909091
24
- IGHD6-13_star_01_19: 0.002840909090909091
25
- IGHD6-13_star_01_2: 0.002840909090909091
26
- IGHD6-13_star_01_20: 0.002840909090909091
27
- IGHD6-13_star_01_3: 0.017045454545454544
28
- IGHD6-13_star_01_4: 0.002840909090909091
29
- IGHD6-13_star_01_5: 0.004734848484848485
30
- IGHD6-13_star_01_6: 0.006628787878787879
31
- IGHD6-13_star_01_7: 0.008522727272727272
32
- IGHD6-13_star_01_8: 0.007305194805194806
33
- IGHD6-13_star_01_9: 0.006087662337662339
34
- insert_left_A: 0.0
35
- insert_left_C: 0.47138047138047134
36
- insert_left_G: 0.101010101010101
37
- insert_left_T: 0.33670033670033667
13
+ IGHD6-13_star_01_0: 0.0006491398896462187
14
+ IGHD6-13_star_01_1: 0.0029211295034079847
15
+ IGHD6-13_star_01_10: 0.0005770132352410833
16
+ IGHD6-13_star_01_11: 0.0005048865808359478
17
+ IGHD6-13_star_01_12: 0.0004327599264308124
18
+ IGHD6-13_star_01_13: 0.00036063327202567696
19
+ IGHD6-13_star_01_14: 0.0002885066176205416
20
+ IGHD6-13_star_01_15: 0.00021637996321540614
21
+ IGHD6-13_star_01_16: 0.0001442533088102707
22
+ IGHD6-13_star_01_17: 7.21266544051353e-05
23
+ IGHD6-13_star_01_18: 0.0006491398896462187
24
+ IGHD6-13_star_01_19: 0.0006491398896462187
25
+ IGHD6-13_star_01_2: 0.00519311911716975
26
+ IGHD6-13_star_01_20: 0.0006491398896462187
27
+ IGHD6-13_star_01_3: 0.006491398896462187
28
+ IGHD6-13_star_01_4: 0.0006491398896462187
29
+ IGHD6-13_star_01_5: 0.0008655198528616249
30
+ IGHD6-13_star_01_6: 0.0010818998160770314
31
+ IGHD6-13_star_01_7: 0.0012982797792924375
32
+ IGHD6-13_star_01_8: 0.0009737098344693282
33
+ IGHD6-13_star_01_9: 0.0006491398896462187
34
+ insert_left_A: 0.11060238800610467
35
+ insert_left_C: 0.4424095520244187
36
+ insert_left_G: 0.1589909327587755
37
+ insert_left_T: 0.2626806715144986
38
38
  - !!python/object:python.hmmwriter.State
39
39
  emissions:
40
40
  probs:
41
- A: 0.8883392155405524
42
- C: 0.03722026148648253
43
- G: 0.03722026148648253
44
- T: 0.03722026148648253
41
+ A: 0.9170723696742016
42
+ C: 0.027642543441932798
43
+ G: 0.027642543441932798
44
+ T: 0.027642543441932798
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: 0.012731481481481483
53
- IGHD6-13_star_01_1: 0.012731481481481483
54
- IGHD6-13_star_01_10: 0.02182539682539683
55
- IGHD6-13_star_01_11: 0.016369047619047623
56
- IGHD6-13_star_01_12: 0.010912698412698417
57
- IGHD6-13_star_01_13: 0.00545634920634921
58
- IGHD6-13_star_01_14: 4.240435163498862e-18
59
- IGHD6-13_star_01_15: 0.012731481481481483
60
- IGHD6-13_star_01_16: 0.012731481481481483
61
- IGHD6-13_star_01_17: 0.012731481481481483
62
- IGHD6-13_star_01_18: 0.012731481481481483
63
- IGHD6-13_star_01_19: 0.012731481481481483
64
- IGHD6-13_star_01_2: 0.012731481481481483
65
- IGHD6-13_star_01_20: 0.012731481481481483
66
- IGHD6-13_star_01_3: 0.0763888888888889
67
- IGHD6-13_star_01_4: 0.012731481481481483
68
- IGHD6-13_star_01_5: 0.02121913580246914
69
- IGHD6-13_star_01_6: 0.029706790123456794
70
- IGHD6-13_star_01_7: 0.03819444444444445
71
- IGHD6-13_star_01_8: 0.03273809523809524
72
- IGHD6-13_star_01_9: 0.02728174603174604
73
- insert_left_A: 0.0
74
- insert_left_C: 0.3072702331961591
75
- insert_left_G: 0.06584362139917695
76
- insert_left_T: 0.21947873799725648
52
+ IGHD6-13_star_01_0: 0.0036630036630036643
53
+ IGHD6-13_star_01_1: 0.01648351648351649
54
+ IGHD6-13_star_01_10: 0.0032560032560032567
55
+ IGHD6-13_star_01_11: 0.0028490028490028496
56
+ IGHD6-13_star_01_12: 0.002442002442002442
57
+ IGHD6-13_star_01_13: 0.002035002035002035
58
+ IGHD6-13_star_01_14: 0.001628001628001628
59
+ IGHD6-13_star_01_15: 0.0012210012210012208
60
+ IGHD6-13_star_01_16: 0.0008140008140008135
61
+ IGHD6-13_star_01_17: 0.0004070004070004065
62
+ IGHD6-13_star_01_18: 0.0036630036630036643
63
+ IGHD6-13_star_01_19: 0.0036630036630036643
64
+ IGHD6-13_star_01_2: 0.029304029304029314
65
+ IGHD6-13_star_01_20: 0.0036630036630036643
66
+ IGHD6-13_star_01_3: 0.03663003663003664
67
+ IGHD6-13_star_01_4: 0.0036630036630036643
68
+ IGHD6-13_star_01_5: 0.004884004884004885
69
+ IGHD6-13_star_01_6: 0.006105006105006107
70
+ IGHD6-13_star_01_7: 0.007326007326007329
71
+ IGHD6-13_star_01_8: 0.005494505494505497
72
+ IGHD6-13_star_01_9: 0.0036630036630036643
73
+ insert_left_A: 0.09726443768996959
74
+ insert_left_C: 0.38905775075987836
75
+ insert_left_G: 0.1398176291793313
76
+ insert_left_T: 0.2310030395136778
77
77
  - !!python/object:python.hmmwriter.State
78
78
  emissions:
79
79
  probs:
80
- A: 0.03722026148648253
81
- C: 0.8883392155405524
82
- G: 0.03722026148648253
83
- T: 0.03722026148648253
80
+ A: 0.027642543441932798
81
+ C: 0.9170723696742016
82
+ G: 0.027642543441932798
83
+ T: 0.027642543441932798
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: 0.012731481481481483
92
- IGHD6-13_star_01_1: 0.012731481481481483
93
- IGHD6-13_star_01_10: 0.02182539682539683
94
- IGHD6-13_star_01_11: 0.016369047619047623
95
- IGHD6-13_star_01_12: 0.010912698412698417
96
- IGHD6-13_star_01_13: 0.00545634920634921
97
- IGHD6-13_star_01_14: 4.240435163498862e-18
98
- IGHD6-13_star_01_15: 0.012731481481481483
99
- IGHD6-13_star_01_16: 0.012731481481481483
100
- IGHD6-13_star_01_17: 0.012731481481481483
101
- IGHD6-13_star_01_18: 0.012731481481481483
102
- IGHD6-13_star_01_19: 0.012731481481481483
103
- IGHD6-13_star_01_2: 0.012731481481481483
104
- IGHD6-13_star_01_20: 0.012731481481481483
105
- IGHD6-13_star_01_3: 0.0763888888888889
106
- IGHD6-13_star_01_4: 0.012731481481481483
107
- IGHD6-13_star_01_5: 0.02121913580246914
108
- IGHD6-13_star_01_6: 0.029706790123456794
109
- IGHD6-13_star_01_7: 0.03819444444444445
110
- IGHD6-13_star_01_8: 0.03273809523809524
111
- IGHD6-13_star_01_9: 0.02728174603174604
112
- insert_left_A: 0.0
113
- insert_left_C: 0.3072702331961591
114
- insert_left_G: 0.06584362139917695
115
- insert_left_T: 0.21947873799725648
91
+ IGHD6-13_star_01_0: 0.0036630036630036643
92
+ IGHD6-13_star_01_1: 0.01648351648351649
93
+ IGHD6-13_star_01_10: 0.0032560032560032567
94
+ IGHD6-13_star_01_11: 0.0028490028490028496
95
+ IGHD6-13_star_01_12: 0.002442002442002442
96
+ IGHD6-13_star_01_13: 0.002035002035002035
97
+ IGHD6-13_star_01_14: 0.001628001628001628
98
+ IGHD6-13_star_01_15: 0.0012210012210012208
99
+ IGHD6-13_star_01_16: 0.0008140008140008135
100
+ IGHD6-13_star_01_17: 0.0004070004070004065
101
+ IGHD6-13_star_01_18: 0.0036630036630036643
102
+ IGHD6-13_star_01_19: 0.0036630036630036643
103
+ IGHD6-13_star_01_2: 0.029304029304029314
104
+ IGHD6-13_star_01_20: 0.0036630036630036643
105
+ IGHD6-13_star_01_3: 0.03663003663003664
106
+ IGHD6-13_star_01_4: 0.0036630036630036643
107
+ IGHD6-13_star_01_5: 0.004884004884004885
108
+ IGHD6-13_star_01_6: 0.006105006105006107
109
+ IGHD6-13_star_01_7: 0.007326007326007329
110
+ IGHD6-13_star_01_8: 0.005494505494505497
111
+ IGHD6-13_star_01_9: 0.0036630036630036643
112
+ insert_left_A: 0.09726443768996959
113
+ insert_left_C: 0.38905775075987836
114
+ insert_left_G: 0.1398176291793313
115
+ insert_left_T: 0.2310030395136778
116
116
  - !!python/object:python.hmmwriter.State
117
117
  emissions:
118
118
  probs:
119
- A: 0.03722026148648253
120
- C: 0.03722026148648253
121
- G: 0.8883392155405524
122
- T: 0.03722026148648253
119
+ A: 0.027642543441932798
120
+ C: 0.027642543441932798
121
+ G: 0.9170723696742016
122
+ T: 0.027642543441932798
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: 0.012731481481481483
131
- IGHD6-13_star_01_1: 0.012731481481481483
132
- IGHD6-13_star_01_10: 0.02182539682539683
133
- IGHD6-13_star_01_11: 0.016369047619047623
134
- IGHD6-13_star_01_12: 0.010912698412698417
135
- IGHD6-13_star_01_13: 0.00545634920634921
136
- IGHD6-13_star_01_14: 4.240435163498862e-18
137
- IGHD6-13_star_01_15: 0.012731481481481483
138
- IGHD6-13_star_01_16: 0.012731481481481483
139
- IGHD6-13_star_01_17: 0.012731481481481483
140
- IGHD6-13_star_01_18: 0.012731481481481483
141
- IGHD6-13_star_01_19: 0.012731481481481483
142
- IGHD6-13_star_01_2: 0.012731481481481483
143
- IGHD6-13_star_01_20: 0.012731481481481483
144
- IGHD6-13_star_01_3: 0.0763888888888889
145
- IGHD6-13_star_01_4: 0.012731481481481483
146
- IGHD6-13_star_01_5: 0.02121913580246914
147
- IGHD6-13_star_01_6: 0.029706790123456794
148
- IGHD6-13_star_01_7: 0.03819444444444445
149
- IGHD6-13_star_01_8: 0.03273809523809524
150
- IGHD6-13_star_01_9: 0.02728174603174604
151
- insert_left_A: 0.0
152
- insert_left_C: 0.3072702331961591
153
- insert_left_G: 0.06584362139917695
154
- insert_left_T: 0.21947873799725648
130
+ IGHD6-13_star_01_0: 0.0036630036630036643
131
+ IGHD6-13_star_01_1: 0.01648351648351649
132
+ IGHD6-13_star_01_10: 0.0032560032560032567
133
+ IGHD6-13_star_01_11: 0.0028490028490028496
134
+ IGHD6-13_star_01_12: 0.002442002442002442
135
+ IGHD6-13_star_01_13: 0.002035002035002035
136
+ IGHD6-13_star_01_14: 0.001628001628001628
137
+ IGHD6-13_star_01_15: 0.0012210012210012208
138
+ IGHD6-13_star_01_16: 0.0008140008140008135
139
+ IGHD6-13_star_01_17: 0.0004070004070004065
140
+ IGHD6-13_star_01_18: 0.0036630036630036643
141
+ IGHD6-13_star_01_19: 0.0036630036630036643
142
+ IGHD6-13_star_01_2: 0.029304029304029314
143
+ IGHD6-13_star_01_20: 0.0036630036630036643
144
+ IGHD6-13_star_01_3: 0.03663003663003664
145
+ IGHD6-13_star_01_4: 0.0036630036630036643
146
+ IGHD6-13_star_01_5: 0.004884004884004885
147
+ IGHD6-13_star_01_6: 0.006105006105006107
148
+ IGHD6-13_star_01_7: 0.007326007326007329
149
+ IGHD6-13_star_01_8: 0.005494505494505497
150
+ IGHD6-13_star_01_9: 0.0036630036630036643
151
+ insert_left_A: 0.09726443768996959
152
+ insert_left_C: 0.38905775075987836
153
+ insert_left_G: 0.1398176291793313
154
+ insert_left_T: 0.2310030395136778
155
155
  - !!python/object:python.hmmwriter.State
156
156
  emissions:
157
157
  probs:
158
- A: 0.03722026148648253
159
- C: 0.03722026148648253
160
- G: 0.03722026148648253
161
- T: 0.8883392155405524
158
+ A: 0.027642543441932798
159
+ C: 0.027642543441932798
160
+ G: 0.027642543441932798
161
+ T: 0.9170723696742016
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: 0.012731481481481483
170
- IGHD6-13_star_01_1: 0.012731481481481483
171
- IGHD6-13_star_01_10: 0.02182539682539683
172
- IGHD6-13_star_01_11: 0.016369047619047623
173
- IGHD6-13_star_01_12: 0.010912698412698417
174
- IGHD6-13_star_01_13: 0.00545634920634921
175
- IGHD6-13_star_01_14: 4.240435163498862e-18
176
- IGHD6-13_star_01_15: 0.012731481481481483
177
- IGHD6-13_star_01_16: 0.012731481481481483
178
- IGHD6-13_star_01_17: 0.012731481481481483
179
- IGHD6-13_star_01_18: 0.012731481481481483
180
- IGHD6-13_star_01_19: 0.012731481481481483
181
- IGHD6-13_star_01_2: 0.012731481481481483
182
- IGHD6-13_star_01_20: 0.012731481481481483
183
- IGHD6-13_star_01_3: 0.0763888888888889
184
- IGHD6-13_star_01_4: 0.012731481481481483
185
- IGHD6-13_star_01_5: 0.02121913580246914
186
- IGHD6-13_star_01_6: 0.029706790123456794
187
- IGHD6-13_star_01_7: 0.03819444444444445
188
- IGHD6-13_star_01_8: 0.03273809523809524
189
- IGHD6-13_star_01_9: 0.02728174603174604
190
- insert_left_A: 0.0
191
- insert_left_C: 0.3072702331961591
192
- insert_left_G: 0.06584362139917695
193
- insert_left_T: 0.21947873799725648
169
+ IGHD6-13_star_01_0: 0.0036630036630036643
170
+ IGHD6-13_star_01_1: 0.01648351648351649
171
+ IGHD6-13_star_01_10: 0.0032560032560032567
172
+ IGHD6-13_star_01_11: 0.0028490028490028496
173
+ IGHD6-13_star_01_12: 0.002442002442002442
174
+ IGHD6-13_star_01_13: 0.002035002035002035
175
+ IGHD6-13_star_01_14: 0.001628001628001628
176
+ IGHD6-13_star_01_15: 0.0012210012210012208
177
+ IGHD6-13_star_01_16: 0.0008140008140008135
178
+ IGHD6-13_star_01_17: 0.0004070004070004065
179
+ IGHD6-13_star_01_18: 0.0036630036630036643
180
+ IGHD6-13_star_01_19: 0.0036630036630036643
181
+ IGHD6-13_star_01_2: 0.029304029304029314
182
+ IGHD6-13_star_01_20: 0.0036630036630036643
183
+ IGHD6-13_star_01_3: 0.03663003663003664
184
+ IGHD6-13_star_01_4: 0.0036630036630036643
185
+ IGHD6-13_star_01_5: 0.004884004884004885
186
+ IGHD6-13_star_01_6: 0.006105006105006107
187
+ IGHD6-13_star_01_7: 0.007326007326007329
188
+ IGHD6-13_star_01_8: 0.005494505494505497
189
+ IGHD6-13_star_01_9: 0.0036630036630036643
190
+ insert_left_A: 0.09726443768996959
191
+ insert_left_C: 0.38905775075987836
192
+ insert_left_G: 0.1398176291793313
193
+ insert_left_T: 0.2310030395136778
194
194
  - !!python/object:python.hmmwriter.State
195
195
  emissions:
196
196
  probs:
197
- A: 0.037220261486482525
198
- C: 0.037220261486482525
199
- G: 0.8883392155405524
200
- T: 0.037220261486482525
197
+ A: 0.027642543441932795
198
+ C: 0.027642543441932795
199
+ G: 0.9170723696742016
200
+ T: 0.027642543441932795
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: 0.9880239520958084
209
+ end: 0.011976047904191614
210
210
  - !!python/object:python.hmmwriter.State
211
211
  emissions:
212
212
  probs:
213
- A: 0.03678838058057706
214
- C: 0.03678838058057706
215
- G: 0.8896348582582688
216
- T: 0.03678838058057706
213
+ A: 0.02855691142867267
214
+ C: 0.02855691142867267
215
+ G: 0.914329265713982
216
+ T: 0.02855691142867267
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: 0.9880239520958084
225
+ end: 0.011976047904191614
226
226
  - !!python/object:python.hmmwriter.State
227
227
  emissions:
228
228
  probs:
229
- A: 0.0363564996746716
230
- C: 0.0363564996746716
231
- G: 0.8909305009759853
232
- T: 0.0363564996746716
229
+ A: 0.029159298902882914
230
+ C: 0.029159298902882914
231
+ G: 0.9125221032913513
232
+ T: 0.029159298902882914
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: 0.9880239520958084
241
+ end: 0.011976047904191614
242
242
  - !!python/object:python.hmmwriter.State
243
243
  emissions:
244
244
  probs:
245
- A: 0.037378097880832795
246
- C: 0.037378097880832795
247
- G: 0.037378097880832795
248
- T: 0.8878657063575016
245
+ A: 0.02511461897635242
246
+ C: 0.02511461897635242
247
+ G: 0.02511461897635242
248
+ T: 0.9246561430709428
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: 0.9880239520958084
257
+ end: 0.011976047904191614
258
258
  - !!python/object:python.hmmwriter.State
259
259
  emissions:
260
260
  probs:
261
- A: 0.8889675443083624
262
- C: 0.03701081856387918
263
- G: 0.03701081856387918
264
- T: 0.03701081856387918
261
+ A: 0.9292558866652231
262
+ C: 0.023581371111592295
263
+ G: 0.023581371111592295
264
+ T: 0.023581371111592295
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: 0.9880239520958084
273
+ end: 0.011976047904191614
274
274
  - !!python/object:python.hmmwriter.State
275
275
  emissions:
276
276
  probs:
277
- A: 0.03695845783322835
278
- C: 0.03695845783322835
279
- G: 0.03695845783322835
280
- T: 0.889124626500315
277
+ A: 0.022566078029007168
278
+ C: 0.022566078029007168
279
+ G: 0.022566078029007168
280
+ T: 0.9323017659129785
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: 0.9880239520958084
289
+ end: 0.011976047904191614
290
290
  - !!python/object:python.hmmwriter.State
291
291
  emissions:
292
292
  probs:
293
- A: 0.8861130718468508
294
- C: 0.03796230938438306
295
- G: 0.03796230938438306
296
- T: 0.03796230938438306
293
+ A: 0.9390241232247338
294
+ C: 0.020325292258422042
295
+ G: 0.020325292258422042
296
+ T: 0.020325292258422042
297
297
  track: nukes
298
298
  extras:
299
299
  ambiguous_char: N
@@ -301,15 +301,15 @@ 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: 0.9880239520958084
305
+ end: 0.011976047904191614
306
306
  - !!python/object:python.hmmwriter.State
307
307
  emissions:
308
308
  probs:
309
- A: 0.03409049982330167
310
- C: 0.03409049982330167
311
- G: 0.897728500530095
312
- T: 0.03409049982330167
309
+ A: 0.01936661271728136
310
+ C: 0.01936661271728136
311
+ G: 0.941900161848156
312
+ T: 0.01936661271728136
313
313
  track: nukes
314
314
  extras:
315
315
  ambiguous_char: N
@@ -317,15 +317,15 @@ states:
317
317
  germline: G
318
318
  name: IGHD6-13_star_01_7
319
319
  transitions:
320
- IGHD6-13_star_01_8: 0.983739837398374
321
- end: 0.016260162601626018
320
+ IGHD6-13_star_01_8: 0.9880239520958084
321
+ end: 0.011976047904191614
322
322
  - !!python/object:python.hmmwriter.State
323
323
  emissions:
324
324
  probs:
325
- A: 0.11411071896396316
326
- C: 0.8098154683933947
327
- G: 0.03803690632132106
328
- T: 0.03803690632132106
325
+ A: 0.06521315117971607
326
+ C: 0.8695736976405679
327
+ G: 0.032606575589858036
328
+ T: 0.032606575589858036
329
329
  track: nukes
330
330
  extras:
331
331
  ambiguous_char: N
@@ -333,15 +333,14 @@ states:
333
333
  germline: C
334
334
  name: IGHD6-13_star_01_8
335
335
  transitions:
336
- IGHD6-13_star_01_9: 0.983739837398374
337
- end: 0.016260162601626018
336
+ IGHD6-13_star_01_9: 1.0
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: 0.9740518962075848
352
+ end: 0.025948103792415196
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: 0.9481037924151696
368
+ end: 0.05189620758483036
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: 0.9221556886227544
384
+ end: 0.07784431137724551
386
385
  - !!python/object:python.hmmwriter.State
387
386
  emissions:
388
387
  probs:
389
- A: 0.8990698269571725
390
- C: 0.03364339101427584
391
- G: 0.03364339101427584
392
- T: 0.03364339101427584
388
+ A: 0.947216920124689
389
+ C: 0.017594359958436973
390
+ G: 0.017594359958436973
391
+ T: 0.017594359958436973
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: 0.8962075848303394
400
+ end: 0.10379241516966067
402
401
  - !!python/object:python.hmmwriter.State
403
402
  emissions:
404
403
  probs:
405
- A: 0.03409049982330167
406
- C: 0.03409049982330167
407
- G: 0.897728500530095
408
- T: 0.03409049982330167
404
+ A: 0.018850382893873953
405
+ C: 0.018850382893873953
406
+ G: 0.9434488513183782
407
+ T: 0.018850382893873953
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: 0.8702594810379242
416
+ end: 0.12974051896207583
418
417
  - !!python/object:python.hmmwriter.State
419
418
  emissions:
420
419
  probs:
421
- A: 0.03453760863232751
422
- C: 0.8963871741030175
423
- G: 0.03453760863232751
424
- T: 0.03453760863232751
420
+ A: 0.028537852644895473
421
+ C: 0.9143864420653136
422
+ G: 0.028537852644895473
423
+ T: 0.028537852644895473
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: 0.844311377245509
432
+ end: 0.155688622754491
434
433
  - !!python/object:python.hmmwriter.State
435
434
  emissions:
436
435
  probs:
437
- A: 0.038121941705899644
438
- C: 0.038121941705899644
439
- G: 0.038121941705899644
440
- T: 0.8856341748823011
436
+ A: 0.030727953865997908
437
+ C: 0.030727953865997908
438
+ G: 0.030727953865997908
439
+ T: 0.9078161384020063
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: 0.9161676646706587
448
+ end: 0.0838323353293413
450
449
  - !!python/object:python.hmmwriter.State
451
450
  emissions:
452
451
  probs:
453
- A: 0.03794160566201621
454
- C: 0.03794160566201621
455
- G: 0.8861751830139514
456
- T: 0.03794160566201621
452
+ A: 0.032620651192821926
453
+ C: 0.032620651192821926
454
+ G: 0.9021380464215343
455
+ T: 0.032620651192821926
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: 0.925748502994012
464
+ end: 0.07425149700598802
466
465
  - !!python/object:python.hmmwriter.State
467
466
  emissions:
468
467
  probs:
469
- A: 0.037761269618132795
470
- C: 0.037761269618132795
471
- G: 0.8867161911456016
472
- T: 0.037761269618132795
468
+ A: 0.031376124255099634
469
+ C: 0.031376124255099634
470
+ G: 0.905871627234701
471
+ T: 0.031376124255099634
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: 0.9353293413173653
480
+ end: 0.06467065868263472
482
481
  - !!python/object:python.hmmwriter.State
483
482
  emissions:
484
483
  probs:
485
- A: 0.037580933574249374
486
- C: 0.037580933574249374
487
- G: 0.037580933574249374
488
- T: 0.8872571992772519
484
+ A: 0.03013159731737736
485
+ C: 0.03013159731737736
486
+ G: 0.03013159731737736
487
+ T: 0.9096052080478679
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: 0.9449101796407186
496
+ end: 0.05508982035928142
498
497
  - !!python/object:python.hmmwriter.State
499
498
  emissions:
500
499
  probs:
501
- A: 0.8877982074089021
502
- C: 0.03740059753036595
503
- G: 0.03740059753036595
504
- T: 0.03740059753036595
500
+ A: 0.9133387888610347
501
+ C: 0.02888707037965508
502
+ G: 0.02888707037965508
503
+ T: 0.02888707037965508
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: 0.9544910179640719
512
+ end: 0.04550898203592813
514
513
  - !!python/object:python.hmmwriter.State
515
514
  emissions:
516
515
  probs:
517
- A: 0.037220261486482525
518
- C: 0.8883392155405524
519
- G: 0.037220261486482525
520
- T: 0.037220261486482525
516
+ A: 0.027642543441932795
517
+ C: 0.9170723696742016
518
+ G: 0.027642543441932795
519
+ T: 0.027642543441932795
521
520
  track: nukes
522
521
  extras:
523
522
  ambiguous_char: N