partis-bcr 1.0.11.post1.dev1__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 (645) hide show
  1. bin/partis +1 -1
  2. bin/partis-test.py +6 -0
  3. bin/partis.py +1 -1
  4. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +645 -127
  7. python/recombinator.py +2 -0
  8. python/treegenerator.py +1 -1
  9. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  10. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +8 -0
  11. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  12. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  13. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  14. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  15. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  16. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  17. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  18. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  19. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +8 -0
  20. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  21. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  22. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  23. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  24. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  25. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  26. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  27. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  28. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  29. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +7 -0
  30. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +7 -0
  31. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +5 -0
  32. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +6 -0
  33. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +7 -0
  34. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  35. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  36. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  37. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +7 -0
  38. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  39. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  40. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  41. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  42. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  43. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  44. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  45. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  46. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  47. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  48. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  49. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  50. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  51. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  52. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  53. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  54. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  55. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  56. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  57. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  58. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  59. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  60. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  61. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  62. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  63. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  64. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  65. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  66. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  67. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  68. test/new-results/annotate-new-simu.yaml +1 -0
  69. test/new-results/cache-new-partition.csv +59 -0
  70. test/new-results/get-selection-metrics-new-simu.yaml +1 -0
  71. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  72. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  73. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  74. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  75. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  76. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  77. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  78. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  79. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  80. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  81. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  82. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  83. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  84. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  85. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  86. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  87. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  88. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  89. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  90. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  91. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  92. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  93. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  94. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  95. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  96. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  97. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  98. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  99. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  100. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  101. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  102. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  103. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  104. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  105. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  106. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  107. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  108. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  109. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  110. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  111. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  112. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  113. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  114. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  115. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  116. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  117. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  118. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  119. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  120. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  121. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  122. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  123. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  124. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  125. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  126. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  127. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  128. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  129. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  130. test/new-results/multi-annotate-new-simu.yaml +1 -0
  131. test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
  132. test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
  133. test/new-results/partition-new-simu/fasttree/iclust-0/log +23 -0
  134. test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
  135. test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
  136. test/new-results/partition-new-simu/fasttree/iclust-1/log +23 -0
  137. test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
  138. test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
  139. test/new-results/partition-new-simu/fasttree/iclust-2/log +22 -0
  140. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  141. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  142. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  143. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  144. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  145. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  146. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  147. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  148. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  149. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  150. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  151. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  152. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  153. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  154. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  155. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  156. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  157. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  158. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  159. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  160. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  161. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  162. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  163. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  164. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  165. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  166. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  167. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  168. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  169. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  170. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  171. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  172. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  173. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  174. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  175. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  176. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  177. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  178. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  179. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  180. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  181. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  182. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  183. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  184. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  185. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  186. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  187. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  188. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  189. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  190. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  191. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  192. test/new-results/partition-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  193. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  194. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  195. test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  196. test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
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  634. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  635. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  636. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  637. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  638. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  639. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  640. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/sw/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: 0.012222222222222223
5
+ per_gene_mute_freq: 0.062318616609175516
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: 0.000334260598697892
14
+ IGHJ4_star_02_1: 0.000417825748372365
15
+ IGHJ4_star_02_10: 0.003259040837304447
16
+ IGHJ4_star_02_11: 0.0027158673644203726
17
+ IGHJ4_star_02_12: 0.002172693891536298
18
+ IGHJ4_star_02_13: 0.0016295204186522235
19
+ IGHJ4_star_02_14: 0.001086346945768149
20
+ IGHJ4_star_02_2: 0.000501390898046838
21
+ IGHJ4_star_02_3: 0.000584956047721311
22
+ IGHJ4_star_02_4: 0.000668521197395784
23
+ IGHJ4_star_02_5: 0.0023398241908852437
24
+ IGHJ4_star_02_6: 0.001504172694140514
25
+ IGHJ4_star_02_7: 0.000668521197395784
26
+ IGHJ4_star_02_8: 0.004345387783072596
27
+ IGHJ4_star_02_9: 0.0038022143101885215
28
+ insert_left_A: 0.1371787966023101
29
+ insert_left_C: 0.3909595703165838
30
+ insert_left_G: 0.15775561609265662
31
+ insert_left_T: 0.2880754728648512
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: 0.9376813833908245
36
+ C: 0.020772872203058505
37
+ G: 0.020772872203058505
38
+ T: 0.020772872203058505
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: 0.0042803638309256275
47
+ IGHJ4_star_02_1: 0.005350454788657034
48
+ IGHJ4_star_02_10: 0.041733547351524874
49
+ IGHJ4_star_02_11: 0.03477795612627073
50
+ IGHJ4_star_02_12: 0.027822364901016583
51
+ IGHJ4_star_02_13: 0.020866773675762437
52
+ IGHJ4_star_02_14: 0.013911182450508291
53
+ IGHJ4_star_02_2: 0.006420545746388441
54
+ IGHJ4_star_02_3: 0.007490636704119849
55
+ IGHJ4_star_02_4: 0.008560727661851255
56
+ IGHJ4_star_02_5: 0.029962546816479394
57
+ IGHJ4_star_02_6: 0.019261637239165325
58
+ IGHJ4_star_02_7: 0.008560727661851255
59
+ IGHJ4_star_02_8: 0.055644729802033166
60
+ IGHJ4_star_02_9: 0.04868913857677901
61
+ insert_left_A: 0.09389671361502348
62
+ insert_left_C: 0.26760563380281693
63
+ insert_left_G: 0.10798122065727701
64
+ insert_left_T: 0.1971830985915493
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: 0.020772872203058505
69
+ C: 0.9376813833908245
70
+ G: 0.020772872203058505
71
+ T: 0.020772872203058505
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: 0.0042803638309256275
80
+ IGHJ4_star_02_1: 0.005350454788657034
81
+ IGHJ4_star_02_10: 0.041733547351524874
82
+ IGHJ4_star_02_11: 0.03477795612627073
83
+ IGHJ4_star_02_12: 0.027822364901016583
84
+ IGHJ4_star_02_13: 0.020866773675762437
85
+ IGHJ4_star_02_14: 0.013911182450508291
86
+ IGHJ4_star_02_2: 0.006420545746388441
87
+ IGHJ4_star_02_3: 0.007490636704119849
88
+ IGHJ4_star_02_4: 0.008560727661851255
89
+ IGHJ4_star_02_5: 0.029962546816479394
90
+ IGHJ4_star_02_6: 0.019261637239165325
91
+ IGHJ4_star_02_7: 0.008560727661851255
92
+ IGHJ4_star_02_8: 0.055644729802033166
93
+ IGHJ4_star_02_9: 0.04868913857677901
94
+ insert_left_A: 0.09389671361502348
95
+ insert_left_C: 0.26760563380281693
96
+ insert_left_G: 0.10798122065727701
97
+ insert_left_T: 0.1971830985915493
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: 0.020772872203058505
102
+ C: 0.020772872203058505
103
+ G: 0.9376813833908245
104
+ T: 0.020772872203058505
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: 0.0042803638309256275
113
+ IGHJ4_star_02_1: 0.005350454788657034
114
+ IGHJ4_star_02_10: 0.041733547351524874
115
+ IGHJ4_star_02_11: 0.03477795612627073
116
+ IGHJ4_star_02_12: 0.027822364901016583
117
+ IGHJ4_star_02_13: 0.020866773675762437
118
+ IGHJ4_star_02_14: 0.013911182450508291
119
+ IGHJ4_star_02_2: 0.006420545746388441
120
+ IGHJ4_star_02_3: 0.007490636704119849
121
+ IGHJ4_star_02_4: 0.008560727661851255
122
+ IGHJ4_star_02_5: 0.029962546816479394
123
+ IGHJ4_star_02_6: 0.019261637239165325
124
+ IGHJ4_star_02_7: 0.008560727661851255
125
+ IGHJ4_star_02_8: 0.055644729802033166
126
+ IGHJ4_star_02_9: 0.04868913857677901
127
+ insert_left_A: 0.09389671361502348
128
+ insert_left_C: 0.26760563380281693
129
+ insert_left_G: 0.10798122065727701
130
+ insert_left_T: 0.1971830985915493
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: 0.020772872203058505
135
+ C: 0.020772872203058505
136
+ G: 0.020772872203058505
137
+ T: 0.9376813833908245
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: 0.0042803638309256275
146
+ IGHJ4_star_02_1: 0.005350454788657034
147
+ IGHJ4_star_02_10: 0.041733547351524874
148
+ IGHJ4_star_02_11: 0.03477795612627073
149
+ IGHJ4_star_02_12: 0.027822364901016583
150
+ IGHJ4_star_02_13: 0.020866773675762437
151
+ IGHJ4_star_02_14: 0.013911182450508291
152
+ IGHJ4_star_02_2: 0.006420545746388441
153
+ IGHJ4_star_02_3: 0.007490636704119849
154
+ IGHJ4_star_02_4: 0.008560727661851255
155
+ IGHJ4_star_02_5: 0.029962546816479394
156
+ IGHJ4_star_02_6: 0.019261637239165325
157
+ IGHJ4_star_02_7: 0.008560727661851255
158
+ IGHJ4_star_02_8: 0.055644729802033166
159
+ IGHJ4_star_02_9: 0.04868913857677901
160
+ insert_left_A: 0.09389671361502348
161
+ insert_left_C: 0.26760563380281693
162
+ insert_left_G: 0.10798122065727701
163
+ insert_left_T: 0.1971830985915493
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: 0.9376813833908245
168
+ C: 0.020772872203058505
169
+ G: 0.020772872203058505
170
+ T: 0.020772872203058505
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: 0.021527821359035165
183
+ C: 0.9354165359228945
184
+ G: 0.021527821359035165
185
+ T: 0.021527821359035165
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: 0.022282770515011822
198
+ C: 0.022282770515011822
199
+ G: 0.022282770515011822
200
+ T: 0.9331516884549645
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: 0.9301541758822008
213
+ C: 0.02328194137259973
214
+ G: 0.02328194137259973
215
+ T: 0.02328194137259973
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: 0.025618297762446802
228
+ C: 0.9231451067126596
229
+ G: 0.025618297762446802
230
+ T: 0.025618297762446802
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: 0.02387872470360638
243
+ C: 0.02387872470360638
244
+ G: 0.02387872470360638
245
+ T: 0.9283638258891809
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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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- C: 0.036013718939189227
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- T: 0.8919588431824323
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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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- T: 0.8925332115265443
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276
276
  track: nukes
277
277
  extras:
278
278
  ambiguous_char: N
@@ -284,10 +284,10 @@ states:
284
284
  - !!python/object:python.hmmwriter.State
285
285
  emissions:
286
286
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287
- A: 0.03699707934069791
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- T: 0.03699707934069791
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288
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291
291
  track: nukes
292
292
  extras:
293
293
  ambiguous_char: N
@@ -299,10 +299,10 @@ states:
299
299
  - !!python/object:python.hmmwriter.State
300
300
  emissions:
301
301
  probs:
302
- A: 0.8890707780854245
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305
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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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317
- A: 0.03695573526901909
318
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319
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320
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318
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319
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320
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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
- A: 0.03693506323317968
333
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333
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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:
346
346
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347
- A: 0.8564050532471041
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- T: 0.0717974733764479
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350
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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
- A: 0.1251410054290541
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364
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- T: 0.01787728648986487
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364
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366
366
  track: nukes
367
367
  extras:
368
368
  ambiguous_char: N
@@ -374,10 +374,10 @@ states:
374
374
  - !!python/object:python.hmmwriter.State
375
375
  emissions:
376
376
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- A: 0.03687304712566145
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- G: 0.03687304712566145
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- T: 0.8893808586230156
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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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394
- G: 0.8894428747305339
395
- 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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407
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- T: 0.03683170305398263
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410
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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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421
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- A: 0.036811031018143224
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425
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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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437
- A: 0.038216245562741315
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- G: 0.885351263311776
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- T: 0.038216245562741315
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440
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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
450
450
  emissions:
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451
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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:
466
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:
481
481
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482
- 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
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
516
  track: nukes
517
517
  extras:
518
518
  ambiguous_char: N
@@ -524,10 +524,10 @@ states:
524
524
  - !!python/object:python.hmmwriter.State
525
525
  emissions:
526
526
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- A: 0.036749014910624996
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- T: 0.036749014910624996
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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
- A: 0.889752955268125
543
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544
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- T: 0.036749014910624996
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546
  track: nukes
547
547
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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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- A: 0.889752955268125
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561
561
  track: nukes
562
562
  extras:
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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573
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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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- A: 0.036749014910624996
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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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- A: 0.036749014910624996
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606
  track: nukes
607
607
  extras:
608
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  ambiguous_char: N
@@ -614,10 +614,10 @@ states:
614
614
  - !!python/object:python.hmmwriter.State
615
615
  emissions:
616
616
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617
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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
- A: 0.036749014910624996
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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
  emissions:
661
661
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662
- A: 0.036749014910624996
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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
  emissions:
676
676
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681
681
  track: nukes
682
682
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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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  - !!python/object:python.hmmwriter.State
705
705
  emissions:
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- A: 0.036749014910624996
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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
  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
  emissions:
736
736
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- A: 0.03833333333333333
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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
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
  emissions:
766
766
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767
- A: 0.036749014910624996
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+ G: 0.015154723428999999
770
+ T: 0.015154723428999999
771
771
  track: nukes
772
772
  extras:
773
773
  ambiguous_char: N
@@ -779,10 +779,10 @@ states:
779
779
  - !!python/object:python.hmmwriter.State
780
780
  emissions:
781
781
  probs:
782
- 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