partis-bcr 1.0.11.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev7__cp312-cp312-manylinux1_x86_64.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 (655) 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 +655 -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. test/paired/new-results/test/simu/igh+igk/igk.yaml +1 -0
  635. test/paired/new-results/test/simu/igh+igl/igh.yaml +1 -0
  636. test/paired/new-results/test/simu/igh+igl/igl.yaml +1 -0
  637. test/paired/new-results/test/simu/igh.yaml +1 -0
  638. test/paired/new-results/test/simu/igk.yaml +1 -0
  639. test/paired/new-results/test/simu/igl.yaml +1 -0
  640. test/paired/new-results/test/simu/meta.yaml +1 -0
  641. test/paired/new-results/test.log +215 -33
  642. test/test.py +6 -0
  643. test/trees.nwk +100 -0
  644. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  646. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  647. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  648. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  649. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  650. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  651. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  652. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  653. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  654. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  655. {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/data/hmm/hmms/IGHJ2_star_01.yaml ADDED
@@ -0,0 +1,1006 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.06521739130434782
4
+ overall_mute_freq: 0.08760869565217394
5
+ per_gene_mute_freq: 0.1196322742685491
6
+ name: IGHJ2_star_01
7
+ states:
8
+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
11
+ name: init
12
+ transitions:
13
+ IGHJ2_star_01_0: 0.0038314176245210726
14
+ IGHJ2_star_01_1: 0.0038314176245210726
15
+ IGHJ2_star_01_10: 0.0038314176245210726
16
+ IGHJ2_star_01_11: 0.0038314176245210726
17
+ IGHJ2_star_01_12: 0.0038314176245210726
18
+ IGHJ2_star_01_13: 0.0038314176245210726
19
+ IGHJ2_star_01_14: 0.0038314176245210726
20
+ IGHJ2_star_01_15: 0.0038314176245210726
21
+ IGHJ2_star_01_16: 0.0038314176245210726
22
+ IGHJ2_star_01_17: 0.0038314176245210726
23
+ IGHJ2_star_01_18: 0.0038314176245210726
24
+ IGHJ2_star_01_19: 0.0038314176245210726
25
+ IGHJ2_star_01_2: 0.0038314176245210726
26
+ IGHJ2_star_01_3: 0.0038314176245210726
27
+ IGHJ2_star_01_4: 0.002554278416347382
28
+ IGHJ2_star_01_5: 0.0012771392081736912
29
+ IGHJ2_star_01_6: 4.2537280636979176e-19
30
+ IGHJ2_star_01_7: 0.0038314176245210726
31
+ IGHJ2_star_01_8: 0.0038314176245210726
32
+ IGHJ2_star_01_9: 0.0038314176245210726
33
+ insert_left_A: 0.18745660726683636
34
+ insert_left_C: 0.2905577412635964
35
+ insert_left_G: 0.21557509835686184
36
+ insert_left_T: 0.2374450358713261
37
+ - !!python/object:python.hmmwriter.State
38
+ emissions:
39
+ probs:
40
+ A: 0.880367725731451
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+ C: 0.039877424756183034
42
+ G: 0.039877424756183034
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+ T: 0.039877424756183034
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+ track: nukes
45
+ extras:
46
+ ambiguous_char: N
47
+ ambiguous_emission_prob: 0.25
48
+ germline: A
49
+ name: insert_left_A
50
+ transitions:
51
+ IGHJ2_star_01_0: 0.010740740740740742
52
+ IGHJ2_star_01_1: 0.010740740740740742
53
+ IGHJ2_star_01_10: 0.010740740740740742
54
+ IGHJ2_star_01_11: 0.010740740740740742
55
+ IGHJ2_star_01_12: 0.010740740740740742
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+ IGHJ2_star_01_13: 0.010740740740740742
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+ IGHJ2_star_01_14: 0.010740740740740742
58
+ IGHJ2_star_01_15: 0.010740740740740742
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+ IGHJ2_star_01_16: 0.010740740740740742
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+ IGHJ2_star_01_17: 0.010740740740740742
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+ IGHJ2_star_01_18: 0.010740740740740742
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+ IGHJ2_star_01_19: 0.010740740740740742
63
+ IGHJ2_star_01_2: 0.010740740740740742
64
+ IGHJ2_star_01_3: 0.010740740740740742
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+ IGHJ2_star_01_4: 0.007160493827160496
66
+ IGHJ2_star_01_5: 0.0035802469135802484
67
+ IGHJ2_star_01_6: 1.192461767189983e-18
68
+ IGHJ2_star_01_7: 0.010740740740740742
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+ IGHJ2_star_01_8: 0.010740740740740742
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+ IGHJ2_star_01_9: 0.010740740740740742
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+ insert_left_A: 0.16241610738255033
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+ insert_left_C: 0.251744966442953
73
+ insert_left_G: 0.18677852348993287
74
+ insert_left_T: 0.20572706935123045
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+ - !!python/object:python.hmmwriter.State
76
+ emissions:
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+ probs:
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+ A: 0.039877424756183034
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+ C: 0.880367725731451
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+ G: 0.039877424756183034
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+ T: 0.039877424756183034
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+ track: nukes
83
+ extras:
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+ ambiguous_char: N
85
+ ambiguous_emission_prob: 0.25
86
+ germline: C
87
+ name: insert_left_C
88
+ transitions:
89
+ IGHJ2_star_01_0: 0.010740740740740742
90
+ IGHJ2_star_01_1: 0.010740740740740742
91
+ IGHJ2_star_01_10: 0.010740740740740742
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+ IGHJ2_star_01_11: 0.010740740740740742
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+ IGHJ2_star_01_12: 0.010740740740740742
94
+ IGHJ2_star_01_13: 0.010740740740740742
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+ IGHJ2_star_01_14: 0.010740740740740742
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+ IGHJ2_star_01_15: 0.010740740740740742
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+ IGHJ2_star_01_16: 0.010740740740740742
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+ IGHJ2_star_01_17: 0.010740740740740742
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+ IGHJ2_star_01_18: 0.010740740740740742
100
+ IGHJ2_star_01_19: 0.010740740740740742
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+ IGHJ2_star_01_2: 0.010740740740740742
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+ IGHJ2_star_01_3: 0.010740740740740742
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+ IGHJ2_star_01_4: 0.007160493827160496
104
+ IGHJ2_star_01_5: 0.0035802469135802484
105
+ IGHJ2_star_01_6: 1.192461767189983e-18
106
+ IGHJ2_star_01_7: 0.010740740740740742
107
+ IGHJ2_star_01_8: 0.010740740740740742
108
+ IGHJ2_star_01_9: 0.010740740740740742
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+ insert_left_A: 0.16241610738255033
110
+ insert_left_C: 0.251744966442953
111
+ insert_left_G: 0.18677852348993287
112
+ insert_left_T: 0.20572706935123045
113
+ - !!python/object:python.hmmwriter.State
114
+ emissions:
115
+ probs:
116
+ A: 0.039877424756183034
117
+ C: 0.039877424756183034
118
+ G: 0.880367725731451
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+ T: 0.039877424756183034
120
+ track: nukes
121
+ extras:
122
+ ambiguous_char: N
123
+ ambiguous_emission_prob: 0.25
124
+ germline: G
125
+ name: insert_left_G
126
+ transitions:
127
+ IGHJ2_star_01_0: 0.010740740740740742
128
+ IGHJ2_star_01_1: 0.010740740740740742
129
+ IGHJ2_star_01_10: 0.010740740740740742
130
+ IGHJ2_star_01_11: 0.010740740740740742
131
+ IGHJ2_star_01_12: 0.010740740740740742
132
+ IGHJ2_star_01_13: 0.010740740740740742
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+ IGHJ2_star_01_14: 0.010740740740740742
134
+ IGHJ2_star_01_15: 0.010740740740740742
135
+ IGHJ2_star_01_16: 0.010740740740740742
136
+ IGHJ2_star_01_17: 0.010740740740740742
137
+ IGHJ2_star_01_18: 0.010740740740740742
138
+ IGHJ2_star_01_19: 0.010740740740740742
139
+ IGHJ2_star_01_2: 0.010740740740740742
140
+ IGHJ2_star_01_3: 0.010740740740740742
141
+ IGHJ2_star_01_4: 0.007160493827160496
142
+ IGHJ2_star_01_5: 0.0035802469135802484
143
+ IGHJ2_star_01_6: 1.192461767189983e-18
144
+ IGHJ2_star_01_7: 0.010740740740740742
145
+ IGHJ2_star_01_8: 0.010740740740740742
146
+ IGHJ2_star_01_9: 0.010740740740740742
147
+ insert_left_A: 0.16241610738255033
148
+ insert_left_C: 0.251744966442953
149
+ insert_left_G: 0.18677852348993287
150
+ insert_left_T: 0.20572706935123045
151
+ - !!python/object:python.hmmwriter.State
152
+ emissions:
153
+ probs:
154
+ A: 0.039877424756183034
155
+ C: 0.039877424756183034
156
+ G: 0.039877424756183034
157
+ T: 0.880367725731451
158
+ track: nukes
159
+ extras:
160
+ ambiguous_char: N
161
+ ambiguous_emission_prob: 0.25
162
+ germline: T
163
+ name: insert_left_T
164
+ transitions:
165
+ IGHJ2_star_01_0: 0.010740740740740742
166
+ IGHJ2_star_01_1: 0.010740740740740742
167
+ IGHJ2_star_01_10: 0.010740740740740742
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+ IGHJ2_star_01_11: 0.010740740740740742
169
+ IGHJ2_star_01_12: 0.010740740740740742
170
+ IGHJ2_star_01_13: 0.010740740740740742
171
+ IGHJ2_star_01_14: 0.010740740740740742
172
+ IGHJ2_star_01_15: 0.010740740740740742
173
+ IGHJ2_star_01_16: 0.010740740740740742
174
+ IGHJ2_star_01_17: 0.010740740740740742
175
+ IGHJ2_star_01_18: 0.010740740740740742
176
+ IGHJ2_star_01_19: 0.010740740740740742
177
+ IGHJ2_star_01_2: 0.010740740740740742
178
+ IGHJ2_star_01_3: 0.010740740740740742
179
+ IGHJ2_star_01_4: 0.007160493827160496
180
+ IGHJ2_star_01_5: 0.0035802469135802484
181
+ IGHJ2_star_01_6: 1.192461767189983e-18
182
+ IGHJ2_star_01_7: 0.010740740740740742
183
+ IGHJ2_star_01_8: 0.010740740740740742
184
+ IGHJ2_star_01_9: 0.010740740740740742
185
+ insert_left_A: 0.16241610738255033
186
+ insert_left_C: 0.251744966442953
187
+ insert_left_G: 0.18677852348993287
188
+ insert_left_T: 0.20572706935123045
189
+ - !!python/object:python.hmmwriter.State
190
+ emissions:
191
+ probs:
192
+ A: 0.03987742475618303
193
+ C: 0.880367725731451
194
+ G: 0.03987742475618303
195
+ T: 0.03987742475618303
196
+ track: nukes
197
+ extras:
198
+ ambiguous_char: N
199
+ ambiguous_emission_prob: 0.25
200
+ germline: C
201
+ name: IGHJ2_star_01_0
202
+ transitions:
203
+ IGHJ2_star_01_1: 1.0
204
+ - !!python/object:python.hmmwriter.State
205
+ emissions:
206
+ probs:
207
+ A: 0.03967714628450346
208
+ C: 0.03967714628450346
209
+ G: 0.03967714628450346
210
+ T: 0.8809685611464896
211
+ track: nukes
212
+ extras:
213
+ ambiguous_char: N
214
+ ambiguous_emission_prob: 0.25
215
+ germline: T
216
+ name: IGHJ2_star_01_1
217
+ transitions:
218
+ IGHJ2_star_01_2: 1.0
219
+ - !!python/object:python.hmmwriter.State
220
+ emissions:
221
+ probs:
222
+ A: 0.8809224433057509
223
+ C: 0.039692518898083055
224
+ G: 0.039692518898083055
225
+ T: 0.039692518898083055
226
+ track: nukes
227
+ extras:
228
+ ambiguous_char: N
229
+ ambiguous_emission_prob: 0.25
230
+ germline: A
231
+ name: IGHJ2_star_01_2
232
+ transitions:
233
+ IGHJ2_star_01_3: 1.0
234
+ - !!python/object:python.hmmwriter.State
235
+ emissions:
236
+ probs:
237
+ A: 0.040645811042755574
238
+ C: 0.8780625668717332
239
+ G: 0.040645811042755574
240
+ T: 0.040645811042755574
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+ track: nukes
242
+ extras:
243
+ ambiguous_char: N
244
+ ambiguous_emission_prob: 0.25
245
+ germline: C
246
+ name: IGHJ2_star_01_3
247
+ transitions:
248
+ IGHJ2_star_01_4: 1.0
249
+ - !!python/object:python.hmmwriter.State
250
+ emissions:
251
+ probs:
252
+ A: 0.03967059698123308
253
+ C: 0.03967059698123308
254
+ G: 0.03967059698123308
255
+ T: 0.8809882090563007
256
+ track: nukes
257
+ extras:
258
+ ambiguous_char: N
259
+ ambiguous_emission_prob: 0.25
260
+ germline: T
261
+ name: IGHJ2_star_01_4
262
+ transitions:
263
+ IGHJ2_star_01_5: 1.0
264
+ - !!python/object:python.hmmwriter.State
265
+ emissions:
266
+ probs:
267
+ A: 0.03961889003749561
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+ C: 0.03961889003749561
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+ T: 0.03961889003749561
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+ track: nukes
272
+ extras:
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+ ambiguous_char: N
274
+ ambiguous_emission_prob: 0.25
275
+ germline: G
276
+ name: IGHJ2_star_01_5
277
+ transitions:
278
+ IGHJ2_star_01_6: 1.0
279
+ - !!python/object:python.hmmwriter.State
280
+ emissions:
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+ probs:
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+ A: 0.03956718309375812
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+ C: 0.03956718309375812
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+ G: 0.8812984507187256
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+ T: 0.03956718309375812
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+ track: nukes
287
+ extras:
288
+ ambiguous_char: N
289
+ ambiguous_emission_prob: 0.25
290
+ germline: G
291
+ name: IGHJ2_star_01_6
292
+ transitions:
293
+ IGHJ2_star_01_7: 1.0
294
+ - !!python/object:python.hmmwriter.State
295
+ emissions:
296
+ probs:
297
+ A: 0.039515476150020636
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+ C: 0.039515476150020636
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+ track: nukes
302
+ extras:
303
+ ambiguous_char: N
304
+ ambiguous_emission_prob: 0.25
305
+ germline: T
306
+ name: IGHJ2_star_01_7
307
+ transitions:
308
+ IGHJ2_star_01_8: 1.0
309
+ - !!python/object:python.hmmwriter.State
310
+ emissions:
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312
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+ T: 0.04192645485370981
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+ track: nukes
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+ extras:
318
+ ambiguous_char: N
319
+ ambiguous_emission_prob: 0.25
320
+ germline: A
321
+ name: IGHJ2_star_01_8
322
+ transitions:
323
+ IGHJ2_star_01_9: 1.0
324
+ - !!python/object:python.hmmwriter.State
325
+ emissions:
326
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327
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329
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+ T: 0.04218258361590067
331
+ track: nukes
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+ extras:
333
+ ambiguous_char: N
334
+ ambiguous_emission_prob: 0.25
335
+ germline: C
336
+ name: IGHJ2_star_01_9
337
+ transitions:
338
+ IGHJ2_star_01_10: 1.0
339
+ - !!python/object:python.hmmwriter.State
340
+ emissions:
341
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342
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+ extras:
348
+ ambiguous_char: N
349
+ ambiguous_emission_prob: 0.25
350
+ germline: T
351
+ name: IGHJ2_star_01_10
352
+ transitions:
353
+ IGHJ2_star_01_11: 1.0
354
+ - !!python/object:python.hmmwriter.State
355
+ emissions:
356
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357
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362
+ extras:
363
+ ambiguous_char: N
364
+ ambiguous_emission_prob: 0.25
365
+ germline: T
366
+ name: IGHJ2_star_01_11
367
+ transitions:
368
+ IGHJ2_star_01_12: 1.0
369
+ - !!python/object:python.hmmwriter.State
370
+ emissions:
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+ ambiguous_char: N
379
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+ germline: C
381
+ name: IGHJ2_star_01_12
382
+ transitions:
383
+ IGHJ2_star_01_13: 1.0
384
+ - !!python/object:python.hmmwriter.State
385
+ emissions:
386
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387
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+ track: nukes
392
+ extras:
393
+ ambiguous_char: N
394
+ ambiguous_emission_prob: 0.25
395
+ germline: G
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+ name: IGHJ2_star_01_13
397
+ transitions:
398
+ IGHJ2_star_01_14: 1.0
399
+ - !!python/object:python.hmmwriter.State
400
+ emissions:
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403
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405
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406
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407
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408
+ ambiguous_char: N
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410
+ germline: A
411
+ name: IGHJ2_star_01_14
412
+ transitions:
413
+ IGHJ2_star_01_15: 1.0
414
+ - !!python/object:python.hmmwriter.State
415
+ emissions:
416
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418
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420
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421
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422
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+ ambiguous_char: N
424
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425
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