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/IGHJ4_star_02.yaml CHANGED
@@ -1,8 +1,8 @@
1
1
  !!python/object:python.hmmwriter.HMM
2
2
  extras:
3
- gene_prob: 0.7
4
- overall_mute_freq: 0.019000000000000003
5
- per_gene_mute_freq: 0.11148736688223958
3
+ gene_prob: 0.6944444444444444
4
+ overall_mute_freq: 0.012499999999999999
5
+ per_gene_mute_freq: 0.06131602620507917
6
6
  name: IGHJ4_star_02
7
7
  states:
8
8
  - !!python/object:python.hmmwriter.State
@@ -10,32 +10,32 @@ states:
10
10
  extras: {}
11
11
  name: init
12
12
  transitions:
13
- IGHJ4_star_02_0: 0.003236245954692557
14
- IGHJ4_star_02_1: 0.003236245954692557
15
- IGHJ4_star_02_10: 0.01699029126213592
16
- IGHJ4_star_02_11: 0.014158576051779935
17
- IGHJ4_star_02_12: 0.011326860841423949
18
- IGHJ4_star_02_13: 0.00849514563106796
19
- IGHJ4_star_02_14: 0.0056634304207119745
20
- IGHJ4_star_02_2: 0.003236245954692557
21
- IGHJ4_star_02_3: 0.003236245954692557
22
- IGHJ4_star_02_4: 0.003236245954692557
23
- IGHJ4_star_02_5: 0.003236245954692557
24
- IGHJ4_star_02_6: 0.003236245954692557
25
- IGHJ4_star_02_7: 0.003236245954692557
26
- IGHJ4_star_02_8: 0.022653721682847898
27
- IGHJ4_star_02_9: 0.01982200647249191
28
- insert_left_A: 0.150390625
29
- insert_left_C: 0.21875
30
- insert_left_G: 0.21875
31
- insert_left_T: 0.287109375
13
+ IGHJ4_star_02_0: 0.00030293698625448993
14
+ IGHJ4_star_02_1: 0.00030293698625448993
15
+ IGHJ4_star_02_10: 0.003408041095363011
16
+ IGHJ4_star_02_11: 0.0028400342461358426
17
+ IGHJ4_star_02_12: 0.002272027396908674
18
+ IGHJ4_star_02_13: 0.0017040205476815055
19
+ IGHJ4_star_02_14: 0.001136013698454337
20
+ IGHJ4_star_02_2: 0.00030293698625448993
21
+ IGHJ4_star_02_3: 0.00030293698625448993
22
+ IGHJ4_star_02_4: 0.0006058739725089799
23
+ IGHJ4_star_02_5: 0.0024234958900359194
24
+ IGHJ4_star_02_6: 0.0014528347482566345
25
+ IGHJ4_star_02_7: 0.0014528347482566345
26
+ IGHJ4_star_02_8: 0.004544054793817348
27
+ IGHJ4_star_02_9: 0.00397604794459018
28
+ insert_left_A: 0.11814671814671815
29
+ insert_left_C: 0.39613899613899617
30
+ insert_left_G: 0.1528957528957529
31
+ insert_left_T: 0.3057915057915058
32
32
  - !!python/object:python.hmmwriter.State
33
33
  emissions:
34
34
  probs:
35
- A: 0.8885126331177604
36
- C: 0.037162455627413195
37
- G: 0.037162455627413195
38
- T: 0.037162455627413195
35
+ A: 0.9386839737949209
36
+ C: 0.020438675401693057
37
+ G: 0.020438675401693057
38
+ T: 0.020438675401693057
39
39
  track: nukes
40
40
  extras:
41
41
  ambiguous_char: N
@@ -43,32 +43,32 @@ states:
43
43
  germline: A
44
44
  name: insert_left_A
45
45
  transitions:
46
- IGHJ4_star_02_0: 0.003236245954692557
47
- IGHJ4_star_02_1: 0.003236245954692557
48
- IGHJ4_star_02_10: 0.01699029126213592
49
- IGHJ4_star_02_11: 0.014158576051779935
50
- IGHJ4_star_02_12: 0.011326860841423949
51
- IGHJ4_star_02_13: 0.00849514563106796
52
- IGHJ4_star_02_14: 0.0056634304207119745
53
- IGHJ4_star_02_2: 0.003236245954692557
54
- IGHJ4_star_02_3: 0.003236245954692557
55
- IGHJ4_star_02_4: 0.003236245954692557
56
- IGHJ4_star_02_5: 0.003236245954692557
57
- IGHJ4_star_02_6: 0.003236245954692557
58
- IGHJ4_star_02_7: 0.003236245954692557
59
- IGHJ4_star_02_8: 0.022653721682847898
60
- IGHJ4_star_02_9: 0.01982200647249191
61
- insert_left_A: 0.150390625
62
- insert_left_C: 0.21875
63
- insert_left_G: 0.21875
64
- insert_left_T: 0.287109375
46
+ IGHJ4_star_02_0: 0.003840006797985154
47
+ IGHJ4_star_02_1: 0.003840006797985154
48
+ IGHJ4_star_02_10: 0.043200076477332976
49
+ IGHJ4_star_02_11: 0.03600006373111082
50
+ IGHJ4_star_02_12: 0.028800050984888654
51
+ IGHJ4_star_02_13: 0.021600038238666488
52
+ IGHJ4_star_02_14: 0.014400025492444327
53
+ IGHJ4_star_02_2: 0.003840006797985154
54
+ IGHJ4_star_02_3: 0.003840006797985154
55
+ IGHJ4_star_02_4: 0.007680013595970308
56
+ IGHJ4_star_02_5: 0.030720054383881232
57
+ IGHJ4_star_02_6: 0.018416025651512336
58
+ IGHJ4_star_02_7: 0.018416025651512336
59
+ IGHJ4_star_02_8: 0.05760010196977731
60
+ IGHJ4_star_02_9: 0.05040008922355515
61
+ insert_left_A: 0.07982804232804233
62
+ insert_left_C: 0.26765873015873015
63
+ insert_left_G: 0.1033068783068783
64
+ insert_left_T: 0.2066137566137566
65
65
  - !!python/object:python.hmmwriter.State
66
66
  emissions:
67
67
  probs:
68
- A: 0.037162455627413195
69
- C: 0.8885126331177604
70
- G: 0.037162455627413195
71
- T: 0.037162455627413195
68
+ A: 0.020438675401693057
69
+ C: 0.9386839737949209
70
+ G: 0.020438675401693057
71
+ T: 0.020438675401693057
72
72
  track: nukes
73
73
  extras:
74
74
  ambiguous_char: N
@@ -76,32 +76,32 @@ states:
76
76
  germline: C
77
77
  name: insert_left_C
78
78
  transitions:
79
- IGHJ4_star_02_0: 0.003236245954692557
80
- IGHJ4_star_02_1: 0.003236245954692557
81
- IGHJ4_star_02_10: 0.01699029126213592
82
- IGHJ4_star_02_11: 0.014158576051779935
83
- IGHJ4_star_02_12: 0.011326860841423949
84
- IGHJ4_star_02_13: 0.00849514563106796
85
- IGHJ4_star_02_14: 0.0056634304207119745
86
- IGHJ4_star_02_2: 0.003236245954692557
87
- IGHJ4_star_02_3: 0.003236245954692557
88
- IGHJ4_star_02_4: 0.003236245954692557
89
- IGHJ4_star_02_5: 0.003236245954692557
90
- IGHJ4_star_02_6: 0.003236245954692557
91
- IGHJ4_star_02_7: 0.003236245954692557
92
- IGHJ4_star_02_8: 0.022653721682847898
93
- IGHJ4_star_02_9: 0.01982200647249191
94
- insert_left_A: 0.150390625
95
- insert_left_C: 0.21875
96
- insert_left_G: 0.21875
97
- insert_left_T: 0.287109375
79
+ IGHJ4_star_02_0: 0.003840006797985154
80
+ IGHJ4_star_02_1: 0.003840006797985154
81
+ IGHJ4_star_02_10: 0.043200076477332976
82
+ IGHJ4_star_02_11: 0.03600006373111082
83
+ IGHJ4_star_02_12: 0.028800050984888654
84
+ IGHJ4_star_02_13: 0.021600038238666488
85
+ IGHJ4_star_02_14: 0.014400025492444327
86
+ IGHJ4_star_02_2: 0.003840006797985154
87
+ IGHJ4_star_02_3: 0.003840006797985154
88
+ IGHJ4_star_02_4: 0.007680013595970308
89
+ IGHJ4_star_02_5: 0.030720054383881232
90
+ IGHJ4_star_02_6: 0.018416025651512336
91
+ IGHJ4_star_02_7: 0.018416025651512336
92
+ IGHJ4_star_02_8: 0.05760010196977731
93
+ IGHJ4_star_02_9: 0.05040008922355515
94
+ insert_left_A: 0.07982804232804233
95
+ insert_left_C: 0.26765873015873015
96
+ insert_left_G: 0.1033068783068783
97
+ insert_left_T: 0.2066137566137566
98
98
  - !!python/object:python.hmmwriter.State
99
99
  emissions:
100
100
  probs:
101
- A: 0.037162455627413195
102
- C: 0.037162455627413195
103
- G: 0.8885126331177604
104
- T: 0.037162455627413195
101
+ A: 0.020438675401693057
102
+ C: 0.020438675401693057
103
+ G: 0.9386839737949209
104
+ T: 0.020438675401693057
105
105
  track: nukes
106
106
  extras:
107
107
  ambiguous_char: N
@@ -109,32 +109,32 @@ states:
109
109
  germline: G
110
110
  name: insert_left_G
111
111
  transitions:
112
- IGHJ4_star_02_0: 0.003236245954692557
113
- IGHJ4_star_02_1: 0.003236245954692557
114
- IGHJ4_star_02_10: 0.01699029126213592
115
- IGHJ4_star_02_11: 0.014158576051779935
116
- IGHJ4_star_02_12: 0.011326860841423949
117
- IGHJ4_star_02_13: 0.00849514563106796
118
- IGHJ4_star_02_14: 0.0056634304207119745
119
- IGHJ4_star_02_2: 0.003236245954692557
120
- IGHJ4_star_02_3: 0.003236245954692557
121
- IGHJ4_star_02_4: 0.003236245954692557
122
- IGHJ4_star_02_5: 0.003236245954692557
123
- IGHJ4_star_02_6: 0.003236245954692557
124
- IGHJ4_star_02_7: 0.003236245954692557
125
- IGHJ4_star_02_8: 0.022653721682847898
126
- IGHJ4_star_02_9: 0.01982200647249191
127
- insert_left_A: 0.150390625
128
- insert_left_C: 0.21875
129
- insert_left_G: 0.21875
130
- insert_left_T: 0.287109375
112
+ IGHJ4_star_02_0: 0.003840006797985154
113
+ IGHJ4_star_02_1: 0.003840006797985154
114
+ IGHJ4_star_02_10: 0.043200076477332976
115
+ IGHJ4_star_02_11: 0.03600006373111082
116
+ IGHJ4_star_02_12: 0.028800050984888654
117
+ IGHJ4_star_02_13: 0.021600038238666488
118
+ IGHJ4_star_02_14: 0.014400025492444327
119
+ IGHJ4_star_02_2: 0.003840006797985154
120
+ IGHJ4_star_02_3: 0.003840006797985154
121
+ IGHJ4_star_02_4: 0.007680013595970308
122
+ IGHJ4_star_02_5: 0.030720054383881232
123
+ IGHJ4_star_02_6: 0.018416025651512336
124
+ IGHJ4_star_02_7: 0.018416025651512336
125
+ IGHJ4_star_02_8: 0.05760010196977731
126
+ IGHJ4_star_02_9: 0.05040008922355515
127
+ insert_left_A: 0.07982804232804233
128
+ insert_left_C: 0.26765873015873015
129
+ insert_left_G: 0.1033068783068783
130
+ insert_left_T: 0.2066137566137566
131
131
  - !!python/object:python.hmmwriter.State
132
132
  emissions:
133
133
  probs:
134
- A: 0.037162455627413195
135
- C: 0.037162455627413195
136
- G: 0.037162455627413195
137
- T: 0.8885126331177604
134
+ A: 0.020438675401693057
135
+ C: 0.020438675401693057
136
+ G: 0.020438675401693057
137
+ T: 0.9386839737949209
138
138
  track: nukes
139
139
  extras:
140
140
  ambiguous_char: N
@@ -142,32 +142,32 @@ states:
142
142
  germline: T
143
143
  name: insert_left_T
144
144
  transitions:
145
- IGHJ4_star_02_0: 0.003236245954692557
146
- IGHJ4_star_02_1: 0.003236245954692557
147
- IGHJ4_star_02_10: 0.01699029126213592
148
- IGHJ4_star_02_11: 0.014158576051779935
149
- IGHJ4_star_02_12: 0.011326860841423949
150
- IGHJ4_star_02_13: 0.00849514563106796
151
- IGHJ4_star_02_14: 0.0056634304207119745
152
- IGHJ4_star_02_2: 0.003236245954692557
153
- IGHJ4_star_02_3: 0.003236245954692557
154
- IGHJ4_star_02_4: 0.003236245954692557
155
- IGHJ4_star_02_5: 0.003236245954692557
156
- IGHJ4_star_02_6: 0.003236245954692557
157
- IGHJ4_star_02_7: 0.003236245954692557
158
- IGHJ4_star_02_8: 0.022653721682847898
159
- IGHJ4_star_02_9: 0.01982200647249191
160
- insert_left_A: 0.150390625
161
- insert_left_C: 0.21875
162
- insert_left_G: 0.21875
163
- insert_left_T: 0.287109375
145
+ IGHJ4_star_02_0: 0.003840006797985154
146
+ IGHJ4_star_02_1: 0.003840006797985154
147
+ IGHJ4_star_02_10: 0.043200076477332976
148
+ IGHJ4_star_02_11: 0.03600006373111082
149
+ IGHJ4_star_02_12: 0.028800050984888654
150
+ IGHJ4_star_02_13: 0.021600038238666488
151
+ IGHJ4_star_02_14: 0.014400025492444327
152
+ IGHJ4_star_02_2: 0.003840006797985154
153
+ IGHJ4_star_02_3: 0.003840006797985154
154
+ IGHJ4_star_02_4: 0.007680013595970308
155
+ IGHJ4_star_02_5: 0.030720054383881232
156
+ IGHJ4_star_02_6: 0.018416025651512336
157
+ IGHJ4_star_02_7: 0.018416025651512336
158
+ IGHJ4_star_02_8: 0.05760010196977731
159
+ IGHJ4_star_02_9: 0.05040008922355515
160
+ insert_left_A: 0.07982804232804233
161
+ insert_left_C: 0.26765873015873015
162
+ insert_left_G: 0.1033068783068783
163
+ insert_left_T: 0.2066137566137566
164
164
  - !!python/object:python.hmmwriter.State
165
165
  emissions:
166
166
  probs:
167
- A: 0.8885126331177604
168
- C: 0.03716245562741319
169
- G: 0.03716245562741319
170
- T: 0.03716245562741319
167
+ A: 0.9386839737949209
168
+ C: 0.020438675401693054
169
+ G: 0.020438675401693054
170
+ T: 0.020438675401693054
171
171
  track: nukes
172
172
  extras:
173
173
  ambiguous_char: N
@@ -179,10 +179,10 @@ states:
179
179
  - !!python/object:python.hmmwriter.State
180
180
  emissions:
181
181
  probs:
182
- A: 0.0369709995127092
183
- C: 0.8890870014618724
184
- G: 0.0369709995127092
185
- T: 0.0369709995127092
182
+ A: 0.02108340829827507
183
+ C: 0.9367497751051748
184
+ G: 0.02108340829827507
185
+ T: 0.02108340829827507
186
186
  track: nukes
187
187
  extras:
188
188
  ambiguous_char: N
@@ -194,10 +194,10 @@ states:
194
194
  - !!python/object:python.hmmwriter.State
195
195
  emissions:
196
196
  probs:
197
- A: 0.0367795433980052
198
- C: 0.0367795433980052
199
- G: 0.0367795433980052
200
- T: 0.8896613698059844
197
+ A: 0.02172814119485708
198
+ C: 0.02172814119485708
199
+ G: 0.02172814119485708
200
+ T: 0.9348155764154288
201
201
  track: nukes
202
202
  extras:
203
203
  ambiguous_char: N
@@ -209,10 +209,10 @@ states:
209
209
  - !!python/object:python.hmmwriter.State
210
210
  emissions:
211
211
  probs:
212
- A: 0.8902357381500964
213
- C: 0.036588087283301214
214
- G: 0.036588087283301214
215
- T: 0.036588087283301214
212
+ A: 0.9328813777256827
213
+ C: 0.022372874091439097
214
+ G: 0.022372874091439097
215
+ T: 0.022372874091439097
216
216
  track: nukes
217
217
  extras:
218
218
  ambiguous_char: N
@@ -224,10 +224,10 @@ states:
224
224
  - !!python/object:python.hmmwriter.State
225
225
  emissions:
226
226
  probs:
227
- A: 0.03639663116859722
228
- C: 0.8908101064942083
229
- G: 0.03639663116859722
230
- T: 0.03639663116859722
227
+ A: 0.02395661355639111
228
+ C: 0.9281301593308267
229
+ G: 0.02395661355639111
230
+ T: 0.02395661355639111
231
231
  track: nukes
232
232
  extras:
233
233
  ambiguous_char: N
@@ -239,10 +239,10 @@ states:
239
239
  - !!python/object:python.hmmwriter.State
240
240
  emissions:
241
241
  probs:
242
- A: 0.03620517505389323
243
- C: 0.03620517505389323
244
- G: 0.03620517505389323
245
- T: 0.8913844748383203
242
+ A: 0.02362807710258229
243
+ C: 0.02362807710258229
244
+ G: 0.02362807710258229
245
+ T: 0.9291157686922531
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: 0.036013718939189227
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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
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272
- A: 0.03582226282448524
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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
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287
- A: 0.03699707934069791
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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
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302
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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
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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
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332
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335
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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:
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346
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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
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- T: 0.01787728648986487
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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:
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376
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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
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392
- A: 0.03685237508982204
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- T: 0.03685237508982204
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395
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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
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- A: 0.03683170305398263
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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:
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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
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441
  track: nukes
442
442
  extras:
443
443
  ambiguous_char: N
@@ -449,10 +449,10 @@ states:
449
449
  - !!python/object:python.hmmwriter.State
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450
  emissions:
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- A: 0.0367696869464644
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- T: 0.0367696869464644
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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:
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466
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- A: 0.036749014910624996
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- T: 0.036749014910624996
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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:
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- A: 0.889752955268125
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484
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- T: 0.036749014910624996
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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
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- A: 0.036749014910624996
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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
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512
- A: 0.036749014910624996
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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
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- A: 0.036749014910624996
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530
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531
531
  track: nukes
532
532
  extras:
533
533
  ambiguous_char: N
@@ -539,10 +539,10 @@ states:
539
539
  - !!python/object:python.hmmwriter.State
540
540
  emissions:
541
541
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542
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543
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546
  track: nukes
547
547
  extras:
548
548
  ambiguous_char: N
@@ -554,10 +554,10 @@ states:
554
554
  - !!python/object:python.hmmwriter.State
555
555
  emissions:
556
556
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561
  track: nukes
562
562
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563
563
  ambiguous_char: N
@@ -569,10 +569,10 @@ states:
569
569
  - !!python/object:python.hmmwriter.State
570
570
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571
571
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572
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576
  track: nukes
577
577
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578
578
  ambiguous_char: N
@@ -584,10 +584,10 @@ states:
584
584
  - !!python/object:python.hmmwriter.State
585
585
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586
586
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- T: 0.036749014910624996
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  track: nukes
592
592
  extras:
593
593
  ambiguous_char: N
@@ -599,10 +599,10 @@ states:
599
599
  - !!python/object:python.hmmwriter.State
600
600
  emissions:
601
601
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  track: nukes
607
607
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608
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  ambiguous_char: N
@@ -614,10 +614,10 @@ states:
614
614
  - !!python/object:python.hmmwriter.State
615
615
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616
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621
621
  track: nukes
622
622
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623
623
  ambiguous_char: N
@@ -629,10 +629,10 @@ states:
629
629
  - !!python/object:python.hmmwriter.State
630
630
  emissions:
631
631
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632
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635
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636
636
  track: nukes
637
637
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638
638
  ambiguous_char: N
@@ -644,10 +644,10 @@ states:
644
644
  - !!python/object:python.hmmwriter.State
645
645
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646
646
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651
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  track: nukes
652
652
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653
653
  ambiguous_char: N
@@ -659,10 +659,10 @@ states:
659
659
  - !!python/object:python.hmmwriter.State
660
660
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661
661
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662
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666
666
  track: nukes
667
667
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668
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  ambiguous_char: N
@@ -674,10 +674,10 @@ states:
674
674
  - !!python/object:python.hmmwriter.State
675
675
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676
676
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681
681
  track: nukes
682
682
  extras:
683
683
  ambiguous_char: N
@@ -689,10 +689,10 @@ states:
689
689
  - !!python/object:python.hmmwriter.State
690
690
  emissions:
691
691
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  track: nukes
697
697
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698
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  ambiguous_char: N
@@ -704,10 +704,10 @@ states:
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704
  - !!python/object:python.hmmwriter.State
705
705
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711
711
  track: nukes
712
712
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713
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  ambiguous_char: N
@@ -719,10 +719,10 @@ states:
719
719
  - !!python/object:python.hmmwriter.State
720
720
  emissions:
721
721
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722
- A: 0.036749014910624996
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726
726
  track: nukes
727
727
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728
728
  ambiguous_char: N
@@ -734,10 +734,10 @@ states:
734
734
  - !!python/object:python.hmmwriter.State
735
735
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736
736
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740
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741
741
  track: nukes
742
742
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743
743
  ambiguous_char: N
@@ -749,10 +749,10 @@ states:
749
749
  - !!python/object:python.hmmwriter.State
750
750
  emissions:
751
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756
756
  track: nukes
757
757
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758
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  ambiguous_char: N
@@ -764,10 +764,10 @@ states:
764
764
  - !!python/object:python.hmmwriter.State
765
765
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766
766
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767
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771
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  track: nukes
772
772
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773
773
  ambiguous_char: N
@@ -779,10 +779,10 @@ states:
779
779
  - !!python/object:python.hmmwriter.State
780
780
  emissions:
781
781
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- A: 0.036749014910624996
783
- C: 0.036749014910624996
784
- G: 0.036749014910624996
785
- T: 0.889752955268125
782
+ A: 0.015154723428999999
783
+ C: 0.015154723428999999
784
+ G: 0.015154723428999999
785
+ T: 0.954535829713
786
786
  track: nukes
787
787
  extras:
788
788
  ambiguous_char: N
@@ -794,10 +794,10 @@ states:
794
794
  - !!python/object:python.hmmwriter.State
795
795
  emissions:
796
796
  probs:
797
- A: 0.036749014910624996
798
- C: 0.889752955268125
799
- G: 0.036749014910624996
800
- T: 0.036749014910624996
797
+ A: 0.015154723428999999
798
+ C: 0.954535829713
799
+ G: 0.015154723428999999
800
+ T: 0.015154723428999999
801
801
  track: nukes
802
802
  extras:
803
803
  ambiguous_char: N
@@ -809,10 +809,10 @@ states:
809
809
  - !!python/object:python.hmmwriter.State
810
810
  emissions:
811
811
  probs:
812
- A: 0.036749014910624996
813
- C: 0.889752955268125
814
- G: 0.036749014910624996
815
- T: 0.036749014910624996
812
+ A: 0.015154723428999999
813
+ C: 0.954535829713
814
+ G: 0.015154723428999999
815
+ T: 0.015154723428999999
816
816
  track: nukes
817
817
  extras:
818
818
  ambiguous_char: N
@@ -824,10 +824,10 @@ states:
824
824
  - !!python/object:python.hmmwriter.State
825
825
  emissions:
826
826
  probs:
827
- A: 0.036749014910624996
828
- C: 0.036749014910624996
829
- G: 0.036749014910624996
830
- T: 0.889752955268125
827
+ A: 0.015154723428999999
828
+ C: 0.015154723428999999
829
+ G: 0.015154723428999999
830
+ T: 0.954535829713
831
831
  track: nukes
832
832
  extras:
833
833
  ambiguous_char: N
@@ -839,10 +839,10 @@ states:
839
839
  - !!python/object:python.hmmwriter.State
840
840
  emissions:
841
841
  probs:
842
- A: 0.036749014910624996
843
- C: 0.889752955268125
844
- G: 0.036749014910624996
845
- T: 0.036749014910624996
842
+ A: 0.015154723428999999
843
+ C: 0.954535829713
844
+ G: 0.015154723428999999
845
+ T: 0.015154723428999999
846
846
  track: nukes
847
847
  extras:
848
848
  ambiguous_char: N
@@ -854,10 +854,10 @@ states:
854
854
  - !!python/object:python.hmmwriter.State
855
855
  emissions:
856
856
  probs:
857
- A: 0.889752955268125
858
- C: 0.036749014910624996
859
- G: 0.036749014910624996
860
- T: 0.036749014910624996
857
+ A: 0.954535829713
858
+ C: 0.015154723428999999
859
+ G: 0.015154723428999999
860
+ T: 0.015154723428999999
861
861
  track: nukes
862
862
  extras:
863
863
  ambiguous_char: N
@@ -869,10 +869,10 @@ states:
869
869
  - !!python/object:python.hmmwriter.State
870
870
  emissions:
871
871
  probs:
872
- A: 0.036749014910624996
873
- C: 0.036749014910624996
874
- G: 0.889752955268125
875
- T: 0.036749014910624996
872
+ A: 0.015154723428999999
873
+ C: 0.015154723428999999
874
+ G: 0.954535829713
875
+ T: 0.015154723428999999
876
876
  track: nukes
877
877
  extras:
878
878
  ambiguous_char: N