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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (644) hide show
  1. bin/partis +1 -1
  2. bin/partis-test.py +6 -0
  3. bin/partis.py +1 -1
  4. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +644 -126
  7. python/recombinator.py +2 -0
  8. python/treegenerator.py +1 -1
  9. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  10. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +8 -0
  11. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  12. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  13. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  14. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  15. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  16. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  17. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  18. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  19. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +8 -0
  20. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  21. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  22. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  23. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  24. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  25. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  26. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  27. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  28. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  29. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +7 -0
  30. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +7 -0
  31. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +5 -0
  32. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +6 -0
  33. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +7 -0
  34. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  35. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  36. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  37. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +7 -0
  38. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  39. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  40. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  41. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  42. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  43. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  44. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  45. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  46. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  47. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  48. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  49. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  50. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  51. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  52. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  53. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  54. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  55. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  56. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  57. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  58. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  59. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  60. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  61. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  62. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  63. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  64. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  65. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  66. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  67. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  68. test/new-results/annotate-new-simu.yaml +1 -0
  69. test/new-results/cache-new-partition.csv +59 -0
  70. test/new-results/get-selection-metrics-new-simu.yaml +1 -0
  71. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  72. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  73. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  74. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  75. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  76. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  77. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  78. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  79. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  80. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  81. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  82. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  83. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  84. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  85. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  86. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  87. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  88. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  89. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  90. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  91. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  92. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  93. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  94. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  95. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  96. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  97. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  98. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  99. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  100. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  101. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  102. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  103. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  104. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  105. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  106. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  107. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  108. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  109. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  110. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  111. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  112. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  113. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  114. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  115. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  116. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  117. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  118. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  119. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  120. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  121. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  122. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  123. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  124. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  125. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  126. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  127. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  128. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  129. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  130. test/new-results/multi-annotate-new-simu.yaml +1 -0
  131. test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
  132. test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
  133. test/new-results/partition-new-simu/fasttree/iclust-0/log +23 -0
  134. test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
  135. test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
  136. test/new-results/partition-new-simu/fasttree/iclust-1/log +23 -0
  137. test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
  138. test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
  139. test/new-results/partition-new-simu/fasttree/iclust-2/log +22 -0
  140. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  141. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  142. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  143. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  144. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  145. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  146. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  147. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  148. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  149. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  150. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  151. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  152. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  153. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  154. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  155. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  156. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  157. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  158. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  159. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  160. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  161. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  162. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  163. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  164. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  165. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  166. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  167. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  168. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  169. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  170. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  171. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  172. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  173. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  174. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  175. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  176. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  177. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  178. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  179. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  180. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  181. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  182. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  183. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  184. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  185. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  186. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  187. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  188. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  189. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  190. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  191. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  192. test/new-results/partition-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  193. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  194. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  195. test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  196. test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
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  632. test/trees.nwk +100 -0
  633. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  634. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  635. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  636. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  637. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  638. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  639. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  640. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  641. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  642. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  643. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  644. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/hmm/hmms/IGHD6-19_star_01.yaml ADDED
@@ -0,0 +1,534 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.027777777777777776
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+ overall_mute_freq: 0.012499999999999999
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+ per_gene_mute_freq: 0.10761556596777501
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+ name: IGHD6-19_star_01
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+ states:
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+ - !!python/object:python.hmmwriter.State
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+ emissions: null
10
+ extras: {}
11
+ name: init
12
+ transitions:
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+ IGHD6-19_star_01_0: 0.023809523809523808
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+ IGHD6-19_star_01_1: 0.023809523809523808
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+ IGHD6-19_star_01_10: 0.023809523809523808
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+ IGHD6-19_star_01_11: 0.023809523809523808
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+ IGHD6-19_star_01_12: 0.023809523809523808
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+ IGHD6-19_star_01_13: 0.023809523809523808
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+ IGHD6-19_star_01_14: 0.023809523809523808
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+ IGHD6-19_star_01_15: 0.023809523809523808
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+ IGHD6-19_star_01_16: 0.023809523809523808
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+ IGHD6-19_star_01_17: 0.023809523809523808
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+ IGHD6-19_star_01_18: 0.023809523809523808
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+ IGHD6-19_star_01_19: 0.023809523809523808
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+ IGHD6-19_star_01_2: 0.023809523809523808
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+ IGHD6-19_star_01_20: 0.023809523809523808
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+ IGHD6-19_star_01_3: 0.023809523809523808
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+ IGHD6-19_star_01_4: 0.023809523809523808
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+ IGHD6-19_star_01_5: 0.023809523809523808
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+ IGHD6-19_star_01_6: 0.023809523809523808
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+ IGHD6-19_star_01_7: 0.023809523809523808
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+ IGHD6-19_star_01_8: 0.023809523809523808
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+ IGHD6-19_star_01_9: 0.023809523809523808
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+ insert_left_A: 0.05673758865248227
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+ insert_left_C: 0.22695035460992907
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+ insert_left_G: 0.08156028368794327
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+ insert_left_T: 0.1347517730496454
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ A: 0.892384434032225
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+ C: 0.03587185532259167
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+ G: 0.03587185532259167
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+ T: 0.03587185532259167
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: A
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+ name: insert_left_A
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+ transitions:
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+ IGHD6-19_star_01_0: 0.023809523809523808
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+ IGHD6-19_star_01_1: 0.023809523809523808
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+ IGHD6-19_star_01_10: 0.023809523809523808
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+ IGHD6-19_star_01_11: 0.023809523809523808
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+ IGHD6-19_star_01_12: 0.023809523809523808
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+ IGHD6-19_star_01_13: 0.023809523809523808
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+ IGHD6-19_star_01_14: 0.023809523809523808
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+ IGHD6-19_star_01_15: 0.023809523809523808
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+ IGHD6-19_star_01_16: 0.023809523809523808
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+ IGHD6-19_star_01_17: 0.023809523809523808
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+ IGHD6-19_star_01_18: 0.023809523809523808
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+ IGHD6-19_star_01_19: 0.023809523809523808
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+ IGHD6-19_star_01_2: 0.023809523809523808
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+ IGHD6-19_star_01_20: 0.023809523809523808
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+ IGHD6-19_star_01_3: 0.023809523809523808
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+ IGHD6-19_star_01_4: 0.023809523809523808
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+ IGHD6-19_star_01_5: 0.023809523809523808
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+ IGHD6-19_star_01_6: 0.023809523809523808
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+ IGHD6-19_star_01_7: 0.023809523809523808
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+ IGHD6-19_star_01_8: 0.023809523809523808
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+ IGHD6-19_star_01_9: 0.023809523809523808
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+ insert_left_A: 0.05673758865248227
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+ insert_left_C: 0.22695035460992907
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+ insert_left_G: 0.08156028368794327
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+ insert_left_T: 0.1347517730496454
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ C: 0.892384434032225
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+ G: 0.03587185532259167
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+ T: 0.03587185532259167
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: C
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+ name: insert_left_C
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+ transitions:
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+ IGHD6-19_star_01_0: 0.023809523809523808
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+ IGHD6-19_star_01_1: 0.023809523809523808
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+ IGHD6-19_star_01_10: 0.023809523809523808
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+ IGHD6-19_star_01_11: 0.023809523809523808
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+ IGHD6-19_star_01_12: 0.023809523809523808
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+ IGHD6-19_star_01_13: 0.023809523809523808
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+ IGHD6-19_star_01_14: 0.023809523809523808
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+ IGHD6-19_star_01_15: 0.023809523809523808
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+ IGHD6-19_star_01_16: 0.023809523809523808
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+ IGHD6-19_star_01_17: 0.023809523809523808
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+ IGHD6-19_star_01_18: 0.023809523809523808
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+ IGHD6-19_star_01_19: 0.023809523809523808
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+ IGHD6-19_star_01_2: 0.023809523809523808
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+ IGHD6-19_star_01_20: 0.023809523809523808
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+ IGHD6-19_star_01_3: 0.023809523809523808
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+ IGHD6-19_star_01_4: 0.023809523809523808
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+ IGHD6-19_star_01_5: 0.023809523809523808
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+ IGHD6-19_star_01_6: 0.023809523809523808
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+ IGHD6-19_star_01_7: 0.023809523809523808
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+ IGHD6-19_star_01_8: 0.023809523809523808
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+ IGHD6-19_star_01_9: 0.023809523809523808
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+ insert_left_A: 0.05673758865248227
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+ insert_left_C: 0.22695035460992907
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+ insert_left_G: 0.08156028368794327
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+ insert_left_T: 0.1347517730496454
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ C: 0.03587185532259167
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+ T: 0.03587185532259167
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: G
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+ name: insert_left_G
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+ transitions:
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+ IGHD6-19_star_01_0: 0.023809523809523808
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+ IGHD6-19_star_01_1: 0.023809523809523808
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+ IGHD6-19_star_01_10: 0.023809523809523808
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+ IGHD6-19_star_01_11: 0.023809523809523808
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+ IGHD6-19_star_01_12: 0.023809523809523808
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+ IGHD6-19_star_01_13: 0.023809523809523808
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+ IGHD6-19_star_01_14: 0.023809523809523808
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+ IGHD6-19_star_01_15: 0.023809523809523808
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+ IGHD6-19_star_01_16: 0.023809523809523808
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+ IGHD6-19_star_01_17: 0.023809523809523808
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+ IGHD6-19_star_01_18: 0.023809523809523808
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+ IGHD6-19_star_01_19: 0.023809523809523808
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+ IGHD6-19_star_01_2: 0.023809523809523808
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+ IGHD6-19_star_01_20: 0.023809523809523808
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+ IGHD6-19_star_01_3: 0.023809523809523808
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+ IGHD6-19_star_01_4: 0.023809523809523808
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+ IGHD6-19_star_01_5: 0.023809523809523808
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+ IGHD6-19_star_01_6: 0.023809523809523808
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+ IGHD6-19_star_01_7: 0.023809523809523808
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+ IGHD6-19_star_01_8: 0.023809523809523808
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+ IGHD6-19_star_01_9: 0.023809523809523808
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+ insert_left_A: 0.05673758865248227
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+ insert_left_C: 0.22695035460992907
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+ insert_left_G: 0.08156028368794327
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+ insert_left_T: 0.1347517730496454
155
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ C: 0.03587185532259167
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+ T: 0.892384434032225
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: T
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+ name: insert_left_T
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+ transitions:
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+ IGHD6-19_star_01_0: 0.023809523809523808
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+ IGHD6-19_star_01_1: 0.023809523809523808
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+ IGHD6-19_star_01_10: 0.023809523809523808
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+ IGHD6-19_star_01_11: 0.023809523809523808
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+ IGHD6-19_star_01_12: 0.023809523809523808
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+ IGHD6-19_star_01_13: 0.023809523809523808
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+ IGHD6-19_star_01_14: 0.023809523809523808
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+ IGHD6-19_star_01_15: 0.023809523809523808
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+ IGHD6-19_star_01_16: 0.023809523809523808
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+ IGHD6-19_star_01_17: 0.023809523809523808
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+ IGHD6-19_star_01_18: 0.023809523809523808
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+ IGHD6-19_star_01_19: 0.023809523809523808
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+ IGHD6-19_star_01_2: 0.023809523809523808
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+ IGHD6-19_star_01_20: 0.023809523809523808
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+ IGHD6-19_star_01_3: 0.023809523809523808
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+ IGHD6-19_star_01_4: 0.023809523809523808
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+ IGHD6-19_star_01_5: 0.023809523809523808
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+ IGHD6-19_star_01_6: 0.023809523809523808
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+ IGHD6-19_star_01_7: 0.023809523809523808
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+ IGHD6-19_star_01_8: 0.023809523809523808
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+ IGHD6-19_star_01_9: 0.023809523809523808
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+ insert_left_A: 0.05673758865248227
191
+ insert_left_C: 0.22695035460992907
192
+ insert_left_G: 0.08156028368794327
193
+ insert_left_T: 0.1347517730496454
194
+ - !!python/object:python.hmmwriter.State
195
+ emissions:
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+ C: 0.03587185532259167
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
204
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+ germline: G
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+ name: IGHD6-19_star_01_0
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+ transitions:
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+ IGHD6-19_star_01_1: 0.9523809523809523
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+ end: 0.047619047619047616
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ track: nukes
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+ extras:
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+ germline: G
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+ name: IGHD6-19_star_01_1
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+ transitions:
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+ IGHD6-19_star_01_2: 0.9523809523809523
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+ end: 0.047619047619047616
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ track: nukes
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+ name: IGHD6-19_star_01_2
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+ end: 0.047619047619047616
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHD6-19_star_01_3
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+ end: 0.047619047619047616
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ track: nukes
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+ transitions:
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+ end: 0.047619047619047616
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ end: 0.047619047619047616
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ track: nukes
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+ end: 0.047619047619047616
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+ - !!python/object:python.hmmwriter.State
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+ track: nukes
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+ end: 0.047619047619047616
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+ - !!python/object:python.hmmwriter.State
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+ track: nukes
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+ - !!python/object:python.hmmwriter.State
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+ track: nukes
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+ end: 0.047619047619047616
354
+ - !!python/object:python.hmmwriter.State
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+ end: 0.047619047619047616
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+ - !!python/object:python.hmmwriter.State
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+ end: 0.047619047619047616
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+ - !!python/object:python.hmmwriter.State
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+ end: 0.047619047619047616
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+ - !!python/object:python.hmmwriter.State
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
420
+ probs:
421
+ A: 0.03587185532259168
422
+ C: 0.892384434032225
423
+ G: 0.03587185532259168
424
+ T: 0.03587185532259168
425
+ track: nukes
426
+ extras:
427
+ ambiguous_char: N
428
+ ambiguous_emission_prob: 0.25
429
+ germline: C
430
+ name: IGHD6-19_star_01_14
431
+ transitions:
432
+ IGHD6-19_star_01_15: 0.9523809523809523
433
+ end: 0.047619047619047616
434
+ - !!python/object:python.hmmwriter.State
435
+ emissions:
436
+ probs:
437
+ A: 0.03587185532259167
438
+ C: 0.03587185532259167
439
+ G: 0.03587185532259167
440
+ T: 0.892384434032225
441
+ track: nukes
442
+ extras:
443
+ ambiguous_char: N
444
+ ambiguous_emission_prob: 0.25
445
+ germline: T
446
+ name: IGHD6-19_star_01_15
447
+ transitions:
448
+ IGHD6-19_star_01_16: 0.9523809523809523
449
+ end: 0.047619047619047616
450
+ - !!python/object:python.hmmwriter.State
451
+ emissions:
452
+ probs:
453
+ A: 0.03587185532259167
454
+ C: 0.03587185532259167
455
+ G: 0.892384434032225
456
+ T: 0.03587185532259167
457
+ track: nukes
458
+ extras:
459
+ ambiguous_char: N
460
+ ambiguous_emission_prob: 0.25
461
+ germline: G
462
+ name: IGHD6-19_star_01_16
463
+ transitions:
464
+ IGHD6-19_star_01_17: 0.9523809523809523
465
+ end: 0.047619047619047616
466
+ - !!python/object:python.hmmwriter.State
467
+ emissions:
468
+ probs:
469
+ A: 0.03587185532259167
470
+ C: 0.03587185532259167
471
+ G: 0.892384434032225
472
+ T: 0.03587185532259167
473
+ track: nukes
474
+ extras:
475
+ ambiguous_char: N
476
+ ambiguous_emission_prob: 0.25
477
+ germline: G
478
+ name: IGHD6-19_star_01_17
479
+ transitions:
480
+ IGHD6-19_star_01_18: 0.9523809523809523
481
+ end: 0.047619047619047616
482
+ - !!python/object:python.hmmwriter.State
483
+ emissions:
484
+ probs:
485
+ A: 0.03587185532259167
486
+ C: 0.03587185532259167
487
+ G: 0.03587185532259167
488
+ T: 0.892384434032225
489
+ track: nukes
490
+ extras:
491
+ ambiguous_char: N
492
+ ambiguous_emission_prob: 0.25
493
+ germline: T
494
+ name: IGHD6-19_star_01_18
495
+ transitions:
496
+ IGHD6-19_star_01_19: 0.9523809523809523
497
+ end: 0.047619047619047616
498
+ - !!python/object:python.hmmwriter.State
499
+ emissions:
500
+ probs:
501
+ A: 0.892384434032225
502
+ C: 0.03587185532259167
503
+ G: 0.03587185532259167
504
+ T: 0.03587185532259167
505
+ track: nukes
506
+ extras:
507
+ ambiguous_char: N
508
+ ambiguous_emission_prob: 0.25
509
+ germline: A
510
+ name: IGHD6-19_star_01_19
511
+ transitions:
512
+ IGHD6-19_star_01_20: 0.9523809523809523
513
+ end: 0.047619047619047616
514
+ - !!python/object:python.hmmwriter.State
515
+ emissions:
516
+ probs:
517
+ A: 0.03587185532259167
518
+ C: 0.892384434032225
519
+ G: 0.03587185532259167
520
+ T: 0.03587185532259167
521
+ track: nukes
522
+ extras:
523
+ ambiguous_char: N
524
+ ambiguous_emission_prob: 0.25
525
+ germline: C
526
+ name: IGHD6-19_star_01_20
527
+ transitions:
528
+ end: 1.0
529
+ tracks:
530
+ nukes:
531
+ - A
532
+ - C
533
+ - G
534
+ - T