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/simu/hmm/j-mean-mute-freqs.csv CHANGED
@@ -1,12 +1,12 @@
1
1
  bin_low_edge,contents,binlabel,error
2
2
  -0.01,0.0,,0.0
3
- 0.0,0.2,,0.1414213562373095
3
+ 0.0,0.5555555555555556,,0.12422599874998833
4
4
  0.01,0.0,,0.0
5
- 0.02,0.4,,0.2
5
+ 0.02,0.2777777777777778,,0.08784104611578832
6
6
  0.03,0.0,,0.0
7
- 0.04,0.0,,0.0
8
- 0.05,0.4,,0.2
9
- 0.06,0.0,,0.0
7
+ 0.04,0.027777777777777776,,0.027777777777777776
8
+ 0.05,0.1111111111111111,,0.05555555555555555
9
+ 0.06,0.027777777777777776,,0.027777777777777776
10
10
  0.07,0.0,,0.0
11
11
  0.08,0.0,,0.0
12
12
  0.09,0.0,,0.0
test/new-results/test/parameters/simu/hmm/j-mean-n-muted.csv CHANGED
@@ -1,9 +1,9 @@
1
1
  bin_low_edge,contents,binlabel,error
2
2
  -1.5,0.0,,0.0
3
- -0.5,2.0,,1.4142135623730951
4
- 0.5,4.0,,2.0
5
- 1.5,4.0,,2.0
6
- 2.5,0.0,,0.0
3
+ -0.5,20.0,,4.47213595499958
4
+ 0.5,10.0,,3.1622776601683795
5
+ 1.5,5.0,,2.23606797749979
6
+ 2.5,1.0,,1.0
7
7
  3.5,0.0,,0.0
8
8
  4.5,0.0,,0.0
9
9
  5.5,0.0,,0.0
test/new-results/test/parameters/simu/hmm/j_gene-dj_insertion-probs.csv CHANGED
@@ -1,3 +1,10 @@
1
1
  dj_insertion,j_gene,count
2
- 19,IGHJ6*02,3
3
- 1,IGHJ4*02,7
2
+ 19,IGHJ6*02,2
3
+ 1,IGHJ4*02,13
4
+ 7,IGHJ4*02,3
5
+ 17,IGHJ6*02,1
6
+ 6,IGHJ4*02,1
7
+ 0,IGHJ1*01,7
8
+ 5,IGHJ4*02,7
9
+ 3,IGHJ4*02,1
10
+ 7,IGHJ1*01,1
test/new-results/test/parameters/simu/hmm/j_gene-j_3p_del-probs.csv CHANGED
@@ -1,3 +1,4 @@
1
1
  j_3p_del,j_gene,count
2
2
  0,IGHJ6*02,3
3
- 0,IGHJ4*02,7
3
+ 0,IGHJ4*02,25
4
+ 0,IGHJ1*01,8
test/new-results/test/parameters/simu/hmm/j_gene-j_5p_del-probs.csv CHANGED
@@ -1,3 +1,8 @@
1
1
  j_5p_del,j_gene,count
2
- 17,IGHJ6*02,3
3
- 8,IGHJ4*02,7
2
+ 17,IGHJ6*02,2
3
+ 8,IGHJ4*02,15
4
+ 4,IGHJ4*02,2
5
+ 15,IGHJ6*02,1
6
+ 3,IGHJ1*01,7
7
+ 5,IGHJ4*02,8
8
+ 6,IGHJ1*01,1
test/new-results/test/parameters/simu/hmm/j_gene-probs.csv CHANGED
@@ -1,3 +1,4 @@
1
1
  j_gene,count
2
2
  IGHJ6*02,3
3
- IGHJ4*02,7
3
+ IGHJ4*02,25
4
+ IGHJ1*01,8
test/new-results/test/parameters/simu/hmm/jf_insertion-probs.csv CHANGED
@@ -1,2 +1,2 @@
1
1
  jf_insertion,count
2
- 0,10
2
+ 0,36
test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD1-20_star_01.csv ADDED
@@ -0,0 +1,9 @@
1
+ position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
2
+ 3,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
3
+ 4,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
4
+ 5,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
5
+ 6,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
6
+ 7,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
7
+ 8,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
8
+ 9,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
9
+ 10,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-16_star_02.csv ADDED
@@ -0,0 +1,30 @@
1
+ position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
2
+ 8,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
3
+ 9,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
4
+ 10,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
5
+ 11,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
6
+ 12,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
7
+ 13,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
8
+ 14,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
9
+ 15,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
10
+ 16,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
11
+ 17,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
12
+ 18,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
13
+ 19,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
14
+ 20,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
15
+ 21,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
16
+ 22,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
17
+ 23,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
18
+ 24,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
19
+ 25,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
20
+ 26,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
21
+ 27,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
22
+ 28,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
23
+ 29,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
24
+ 30,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
25
+ 31,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
26
+ 32,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
27
+ 33,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
28
+ 34,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
29
+ 35,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
30
+ 36,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-22_star_01.csv ADDED
@@ -0,0 +1,32 @@
1
+ position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
2
+ 0,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
3
+ 1,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0
4
+ 2,0.0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
5
+ 3,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0
6
+ 4,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0
7
+ 5,0.0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
8
+ 6,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
9
+ 7,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0
10
+ 8,0.0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
11
+ 9,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0
12
+ 10,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
13
+ 11,0.0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
14
+ 12,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0
15
+ 13,0.0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
16
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test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-13_star_01.csv CHANGED
@@ -1,17 +1,20 @@
1
1
  position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
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18
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19
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20
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test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-19_star_01.csv ADDED
@@ -0,0 +1,22 @@
1
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2
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test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ1_star_01.csv ADDED
@@ -0,0 +1,50 @@
1
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test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ4_star_02.csv CHANGED
@@ -1,41 +1,45 @@
1
1
  position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
2
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3
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test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ6_star_02.csv CHANGED
@@ -1,4 +1,6 @@
1
1
  position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
2
+ 15,0.0,0.0,0.504622638711,1.0,1,0.5773502691896258,1.0,0.0,0,0.0,0.504622638711,0.0,0,0.0,0.504622638711,0.0,0,0.0,0.504622638711
3
+ 16,1.0,0.5773502691896258,1.0,0.0,0,0.0,0.504622638711,0.0,0,0.0,0.504622638711,1.0,1,0.5773502691896258,1.0,0.0,0,0.0,0.504622638711
2
4
  17,0.0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,1.0,3,0.7598356856515925,1.0,0.0,0,0.0,0.420398101924
3
5
  18,0.0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,1.0,3,0.7598356856515925,1.0,0.0,0,0.0,0.420398101924
4
6
  19,0.0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,1.0,3,0.7598356856515925,1.0