partis-bcr 1.0.11__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__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.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/RECORD +655 -128
  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
  197. test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
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  635. test/paired/new-results/test/simu/igh+igk/igk.yaml +1 -0
  636. test/paired/new-results/test/simu/igh+igl/igh.yaml +1 -0
  637. test/paired/new-results/test/simu/igh+igl/igl.yaml +1 -0
  638. test/paired/new-results/test/simu/igh.yaml +1 -0
  639. test/paired/new-results/test/simu/igk.yaml +1 -0
  640. test/paired/new-results/test/simu/igl.yaml +1 -0
  641. test/paired/new-results/test/simu/meta.yaml +1 -0
  642. test/paired/new-results/test.log +225 -40
  643. test/test.py +6 -0
  644. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  645. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  646. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  647. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  648. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/gctree-run.py +0 -0
  649. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  650. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/parse-output.py +0 -0
  651. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/split-loci.py +0 -0
  652. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/WHEEL +0 -0
  653. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/entry_points.txt +0 -0
  654. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/licenses/COPYING +0 -0
  655. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/data/sw/hmms/IGHJ3_star_02.yaml ADDED
@@ -0,0 +1,946 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.10869565217391304
4
+ overall_mute_freq: 0.08956521739130437
5
+ per_gene_mute_freq: 0.12501075352277902
6
+ name: IGHJ3_star_02
7
+ states:
8
+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
11
+ name: init
12
+ transitions:
13
+ IGHJ3_star_02_0: 0.006216006216006216
14
+ IGHJ3_star_02_1: 0.006216006216006216
15
+ IGHJ3_star_02_10: 0.003108003108003108
16
+ IGHJ3_star_02_11: 0.003108003108003108
17
+ IGHJ3_star_02_12: 0.003108003108003108
18
+ IGHJ3_star_02_13: 0.003108003108003108
19
+ IGHJ3_star_02_14: 0.003108003108003108
20
+ IGHJ3_star_02_15: 0.003108003108003108
21
+ IGHJ3_star_02_16: 0.003108003108003108
22
+ IGHJ3_star_02_2: 0.006216006216006216
23
+ IGHJ3_star_02_3: 0.006216006216006216
24
+ IGHJ3_star_02_4: 0.003108003108003108
25
+ IGHJ3_star_02_5: 0.002331002331002331
26
+ IGHJ3_star_02_6: 0.001554001554001554
27
+ IGHJ3_star_02_7: 0.000777000777000777
28
+ IGHJ3_star_02_8: 0.003108003108003108
29
+ IGHJ3_star_02_9: 0.003108003108003108
30
+ insert_left_A: 0.20421607378129117
31
+ insert_left_C: 0.2893061045234958
32
+ insert_left_G: 0.21102327624066755
33
+ insert_left_T: 0.23484848484848486
34
+ - !!python/object:python.hmmwriter.State
35
+ emissions:
36
+ probs:
37
+ A: 0.874989246477221
38
+ C: 0.041670251174259675
39
+ G: 0.041670251174259675
40
+ T: 0.041670251174259675
41
+ track: nukes
42
+ extras:
43
+ ambiguous_char: N
44
+ ambiguous_emission_prob: 0.25
45
+ germline: A
46
+ name: insert_left_A
47
+ transitions:
48
+ IGHJ3_star_02_0: 0.017908017908017913
49
+ IGHJ3_star_02_1: 0.017908017908017913
50
+ IGHJ3_star_02_10: 0.008954008954008956
51
+ IGHJ3_star_02_11: 0.008954008954008956
52
+ IGHJ3_star_02_12: 0.008954008954008956
53
+ IGHJ3_star_02_13: 0.008954008954008956
54
+ IGHJ3_star_02_14: 0.008954008954008956
55
+ IGHJ3_star_02_15: 0.008954008954008956
56
+ IGHJ3_star_02_16: 0.008954008954008956
57
+ IGHJ3_star_02_2: 0.017908017908017913
58
+ IGHJ3_star_02_3: 0.017908017908017913
59
+ IGHJ3_star_02_4: 0.008954008954008956
60
+ IGHJ3_star_02_5: 0.006715506715506718
61
+ IGHJ3_star_02_6: 0.004477004477004478
62
+ IGHJ3_star_02_7: 0.002238502238502239
63
+ IGHJ3_star_02_8: 0.008954008954008956
64
+ IGHJ3_star_02_9: 0.008954008954008956
65
+ insert_left_A: 0.17943409247757072
66
+ insert_left_C: 0.2541982976765585
67
+ insert_left_G: 0.18541522889348974
68
+ insert_left_T: 0.20634920634920634
69
+ - !!python/object:python.hmmwriter.State
70
+ emissions:
71
+ probs:
72
+ A: 0.041670251174259675
73
+ C: 0.874989246477221
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+ G: 0.041670251174259675
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+ T: 0.041670251174259675
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+ track: nukes
77
+ extras:
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+ ambiguous_char: N
79
+ ambiguous_emission_prob: 0.25
80
+ germline: C
81
+ name: insert_left_C
82
+ transitions:
83
+ IGHJ3_star_02_0: 0.017908017908017913
84
+ IGHJ3_star_02_1: 0.017908017908017913
85
+ IGHJ3_star_02_10: 0.008954008954008956
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+ IGHJ3_star_02_11: 0.008954008954008956
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+ IGHJ3_star_02_12: 0.008954008954008956
88
+ IGHJ3_star_02_13: 0.008954008954008956
89
+ IGHJ3_star_02_14: 0.008954008954008956
90
+ IGHJ3_star_02_15: 0.008954008954008956
91
+ IGHJ3_star_02_16: 0.008954008954008956
92
+ IGHJ3_star_02_2: 0.017908017908017913
93
+ IGHJ3_star_02_3: 0.017908017908017913
94
+ IGHJ3_star_02_4: 0.008954008954008956
95
+ IGHJ3_star_02_5: 0.006715506715506718
96
+ IGHJ3_star_02_6: 0.004477004477004478
97
+ IGHJ3_star_02_7: 0.002238502238502239
98
+ IGHJ3_star_02_8: 0.008954008954008956
99
+ IGHJ3_star_02_9: 0.008954008954008956
100
+ insert_left_A: 0.17943409247757072
101
+ insert_left_C: 0.2541982976765585
102
+ insert_left_G: 0.18541522889348974
103
+ insert_left_T: 0.20634920634920634
104
+ - !!python/object:python.hmmwriter.State
105
+ emissions:
106
+ probs:
107
+ A: 0.041670251174259675
108
+ C: 0.041670251174259675
109
+ G: 0.874989246477221
110
+ T: 0.041670251174259675
111
+ track: nukes
112
+ extras:
113
+ ambiguous_char: N
114
+ ambiguous_emission_prob: 0.25
115
+ germline: G
116
+ name: insert_left_G
117
+ transitions:
118
+ IGHJ3_star_02_0: 0.017908017908017913
119
+ IGHJ3_star_02_1: 0.017908017908017913
120
+ IGHJ3_star_02_10: 0.008954008954008956
121
+ IGHJ3_star_02_11: 0.008954008954008956
122
+ IGHJ3_star_02_12: 0.008954008954008956
123
+ IGHJ3_star_02_13: 0.008954008954008956
124
+ IGHJ3_star_02_14: 0.008954008954008956
125
+ IGHJ3_star_02_15: 0.008954008954008956
126
+ IGHJ3_star_02_16: 0.008954008954008956
127
+ IGHJ3_star_02_2: 0.017908017908017913
128
+ IGHJ3_star_02_3: 0.017908017908017913
129
+ IGHJ3_star_02_4: 0.008954008954008956
130
+ IGHJ3_star_02_5: 0.006715506715506718
131
+ IGHJ3_star_02_6: 0.004477004477004478
132
+ IGHJ3_star_02_7: 0.002238502238502239
133
+ IGHJ3_star_02_8: 0.008954008954008956
134
+ IGHJ3_star_02_9: 0.008954008954008956
135
+ insert_left_A: 0.17943409247757072
136
+ insert_left_C: 0.2541982976765585
137
+ insert_left_G: 0.18541522889348974
138
+ insert_left_T: 0.20634920634920634
139
+ - !!python/object:python.hmmwriter.State
140
+ emissions:
141
+ probs:
142
+ A: 0.041670251174259675
143
+ C: 0.041670251174259675
144
+ G: 0.041670251174259675
145
+ T: 0.874989246477221
146
+ track: nukes
147
+ extras:
148
+ ambiguous_char: N
149
+ ambiguous_emission_prob: 0.25
150
+ germline: T
151
+ name: insert_left_T
152
+ transitions:
153
+ IGHJ3_star_02_0: 0.017908017908017913
154
+ IGHJ3_star_02_1: 0.017908017908017913
155
+ IGHJ3_star_02_10: 0.008954008954008956
156
+ IGHJ3_star_02_11: 0.008954008954008956
157
+ IGHJ3_star_02_12: 0.008954008954008956
158
+ IGHJ3_star_02_13: 0.008954008954008956
159
+ IGHJ3_star_02_14: 0.008954008954008956
160
+ IGHJ3_star_02_15: 0.008954008954008956
161
+ IGHJ3_star_02_16: 0.008954008954008956
162
+ IGHJ3_star_02_2: 0.017908017908017913
163
+ IGHJ3_star_02_3: 0.017908017908017913
164
+ IGHJ3_star_02_4: 0.008954008954008956
165
+ IGHJ3_star_02_5: 0.006715506715506718
166
+ IGHJ3_star_02_6: 0.004477004477004478
167
+ IGHJ3_star_02_7: 0.002238502238502239
168
+ IGHJ3_star_02_8: 0.008954008954008956
169
+ IGHJ3_star_02_9: 0.008954008954008956
170
+ insert_left_A: 0.17943409247757072
171
+ insert_left_C: 0.2541982976765585
172
+ insert_left_G: 0.18541522889348974
173
+ insert_left_T: 0.20634920634920634
174
+ - !!python/object:python.hmmwriter.State
175
+ emissions:
176
+ probs:
177
+ A: 0.04167025117425967
178
+ C: 0.04167025117425967
179
+ G: 0.04167025117425967
180
+ T: 0.874989246477221
181
+ track: nukes
182
+ extras:
183
+ ambiguous_char: N
184
+ ambiguous_emission_prob: 0.25
185
+ germline: T
186
+ name: IGHJ3_star_02_0
187
+ transitions:
188
+ IGHJ3_star_02_1: 1.0
189
+ - !!python/object:python.hmmwriter.State
190
+ emissions:
191
+ probs:
192
+ A: 0.04148815692430586
193
+ C: 0.04148815692430586
194
+ G: 0.8755355292270824
195
+ T: 0.04148815692430586
196
+ track: nukes
197
+ extras:
198
+ ambiguous_char: N
199
+ ambiguous_emission_prob: 0.25
200
+ germline: G
201
+ name: IGHJ3_star_02_1
202
+ transitions:
203
+ IGHJ3_star_02_2: 1.0
204
+ - !!python/object:python.hmmwriter.State
205
+ emissions:
206
+ probs:
207
+ A: 0.8749903218294989
208
+ C: 0.041669892723500364
209
+ G: 0.041669892723500364
210
+ T: 0.041669892723500364
211
+ track: nukes
212
+ extras:
213
+ ambiguous_char: N
214
+ ambiguous_emission_prob: 0.25
215
+ germline: A
216
+ name: IGHJ3_star_02_2
217
+ transitions:
218
+ IGHJ3_star_02_3: 1.0
219
+ - !!python/object:python.hmmwriter.State
220
+ emissions:
221
+ probs:
222
+ A: 0.04125093996084071
223
+ C: 0.04125093996084071
224
+ G: 0.04125093996084071
225
+ T: 0.8762471801174778
226
+ track: nukes
227
+ extras:
228
+ ambiguous_char: N
229
+ ambiguous_emission_prob: 0.25
230
+ germline: T
231
+ name: IGHJ3_star_02_3
232
+ transitions:
233
+ IGHJ3_star_02_4: 1.0
234
+ - !!python/object:python.hmmwriter.State
235
+ emissions:
236
+ probs:
237
+ A: 0.04166953427274107
238
+ C: 0.04166953427274107
239
+ G: 0.8749913971817768
240
+ T: 0.04166953427274107
241
+ track: nukes
242
+ extras:
243
+ ambiguous_char: N
244
+ ambiguous_emission_prob: 0.25
245
+ germline: G
246
+ name: IGHJ3_star_02_4
247
+ transitions:
248
+ IGHJ3_star_02_5: 1.0
249
+ - !!python/object:python.hmmwriter.State
250
+ emissions:
251
+ probs:
252
+ A: 0.04166935504736142
253
+ C: 0.8749919348579157
254
+ G: 0.04166935504736142
255
+ T: 0.04166935504736142
256
+ track: nukes
257
+ extras:
258
+ ambiguous_char: N
259
+ ambiguous_emission_prob: 0.25
260
+ germline: C
261
+ name: IGHJ3_star_02_5
262
+ transitions:
263
+ IGHJ3_star_02_6: 1.0
264
+ - !!python/object:python.hmmwriter.State
265
+ emissions:
266
+ probs:
267
+ A: 0.04069969488640676
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+ C: 0.04069969488640676
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+ G: 0.04069969488640676
270
+ T: 0.8779009153407797
271
+ track: nukes
272
+ extras:
273
+ ambiguous_char: N
274
+ ambiguous_emission_prob: 0.25
275
+ germline: T
276
+ name: IGHJ3_star_02_6
277
+ transitions:
278
+ IGHJ3_star_02_7: 1.0
279
+ - !!python/object:python.hmmwriter.State
280
+ emissions:
281
+ probs:
282
+ A: 0.041668996596602115
283
+ C: 0.041668996596602115
284
+ G: 0.041668996596602115
285
+ T: 0.8749930102101937
286
+ track: nukes
287
+ extras:
288
+ ambiguous_char: N
289
+ ambiguous_emission_prob: 0.25
290
+ germline: T
291
+ name: IGHJ3_star_02_7
292
+ transitions:
293
+ IGHJ3_star_02_8: 1.0
294
+ - !!python/object:python.hmmwriter.State
295
+ emissions:
296
+ probs:
297
+ A: 0.04037617612378913
298
+ C: 0.04037617612378913
299
+ G: 0.04037617612378913
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+ T: 0.8788714716286326
301
+ track: nukes
302
+ extras:
303
+ ambiguous_char: N
304
+ ambiguous_emission_prob: 0.25
305
+ germline: T
306
+ name: IGHJ3_star_02_8
307
+ transitions:
308
+ IGHJ3_star_02_9: 1.0
309
+ - !!python/object:python.hmmwriter.State
310
+ emissions:
311
+ probs:
312
+ A: 0.04166863814584282
313
+ C: 0.04166863814584282
314
+ G: 0.04166863814584282
315
+ T: 0.8749940855624716
316
+ track: nukes
317
+ extras:
318
+ ambiguous_char: N
319
+ ambiguous_emission_prob: 0.25
320
+ germline: T
321
+ name: IGHJ3_star_02_9
322
+ transitions:
323
+ IGHJ3_star_02_10: 1.0
324
+ - !!python/object:python.hmmwriter.State
325
+ emissions:
326
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327
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329
+ G: 0.8562446232386105
330
+ T: 0.04791845892046316
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+ track: nukes
332
+ extras:
333
+ ambiguous_char: N
334
+ ambiguous_emission_prob: 0.25
335
+ germline: G
336
+ name: IGHJ3_star_02_10
337
+ transitions:
338
+ IGHJ3_star_02_11: 1.0
339
+ - !!python/object:python.hmmwriter.State
340
+ emissions:
341
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342
+ A: 0.880327306060412
343
+ C: 0.039890897979862686
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346
+ track: nukes
347
+ extras:
348
+ ambiguous_char: N
349
+ ambiguous_emission_prob: 0.25
350
+ germline: A
351
+ name: IGHJ3_star_02_11
352
+ transitions:
353
+ IGHJ3_star_02_12: 1.0
354
+ - !!python/object:python.hmmwriter.State
355
+ emissions:
356
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357
+ A: 0.04166810046970387
358
+ C: 0.04166810046970387
359
+ G: 0.04166810046970387
360
+ T: 0.8749956985908884
361
+ track: nukes
362
+ extras:
363
+ ambiguous_char: N
364
+ ambiguous_emission_prob: 0.25
365
+ germline: T
366
+ name: IGHJ3_star_02_12
367
+ transitions:
368
+ IGHJ3_star_02_13: 1.0
369
+ - !!python/object:python.hmmwriter.State
370
+ emissions:
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373
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374
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+ T: 0.041667921244324224
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+ track: nukes
377
+ extras:
378
+ ambiguous_char: N
379
+ ambiguous_emission_prob: 0.25
380
+ germline: A
381
+ name: IGHJ3_star_02_13
382
+ transitions:
383
+ IGHJ3_star_02_14: 1.0
384
+ - !!python/object:python.hmmwriter.State
385
+ emissions:
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387
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+ C: 0.041667742018944576
389
+ G: 0.041667742018944576
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+ T: 0.8749967739431663
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+ track: nukes
392
+ extras:
393
+ ambiguous_char: N
394
+ ambiguous_emission_prob: 0.25
395
+ germline: T
396
+ name: IGHJ3_star_02_14
397
+ transitions:
398
+ IGHJ3_star_02_15: 1.0
399
+ - !!python/object:python.hmmwriter.State
400
+ emissions:
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402
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403
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404
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405
+ T: 0.04166756279356491
406
+ track: nukes
407
+ extras:
408
+ ambiguous_char: N
409
+ ambiguous_emission_prob: 0.25
410
+ germline: C
411
+ name: IGHJ3_star_02_15
412
+ transitions:
413
+ IGHJ3_star_02_16: 1.0
414
+ - !!python/object:python.hmmwriter.State
415
+ emissions:
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417
+ A: 0.0390821010733186
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+ C: 0.0390821010733186
419
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+ T: 0.8827536967800442
421
+ track: nukes
422
+ extras:
423
+ ambiguous_char: N
424
+ ambiguous_emission_prob: 0.25
425
+ germline: T
426
+ name: IGHJ3_star_02_16
427
+ transitions:
428
+ IGHJ3_star_02_17: 1.0
429
+ - !!python/object:python.hmmwriter.State
430
+ emissions:
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432
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435
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
439
+ ambiguous_emission_prob: 0.25
440
+ germline: G
441
+ name: IGHJ3_star_02_17
442
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