partis-bcr 1.0.11.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl → 1.0.11.post1.dev7__cp312-cp312-macosx_10_13_universal2.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (645) hide show
  1. bin/partis +1 -1
  2. bin/partis-test.py +6 -0
  3. bin/partis.py +1 -1
  4. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +645 -127
  7. python/recombinator.py +2 -0
  8. python/treegenerator.py +1 -1
  9. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  10. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +8 -0
  11. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  12. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  13. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  14. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  15. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  16. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  17. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  18. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  19. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +8 -0
  20. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  21. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  22. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  23. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  24. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  25. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  26. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  27. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  28. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  29. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +7 -0
  30. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +7 -0
  31. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +5 -0
  32. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +6 -0
  33. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +7 -0
  34. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  35. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  36. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  37. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +7 -0
  38. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  39. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  40. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  41. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  42. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  43. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  44. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  45. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  46. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  47. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  48. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  49. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  50. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  51. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  52. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  53. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  54. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  55. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  56. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  57. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  58. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  59. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  60. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  61. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  62. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  63. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  64. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  65. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  66. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  67. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  68. test/new-results/annotate-new-simu.yaml +1 -0
  69. test/new-results/cache-new-partition.csv +59 -0
  70. test/new-results/get-selection-metrics-new-simu.yaml +1 -0
  71. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  72. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  73. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  74. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  75. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  76. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  77. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  78. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  79. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  80. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  81. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  82. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  83. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  84. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  85. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  86. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  87. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  88. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  89. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  90. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  91. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  92. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  93. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  94. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  95. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  96. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  97. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  98. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  99. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  100. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  101. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  102. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  103. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  104. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  105. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  106. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  107. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  108. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  109. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  110. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  111. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  112. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  113. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  114. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  115. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  116. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  117. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  118. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  119. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  120. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  121. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  122. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  123. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  124. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  125. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  126. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  127. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  128. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  129. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  130. test/new-results/multi-annotate-new-simu.yaml +1 -0
  131. test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
  132. test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
  133. test/new-results/partition-new-simu/fasttree/iclust-0/log +23 -0
  134. test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
  135. test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
  136. test/new-results/partition-new-simu/fasttree/iclust-1/log +23 -0
  137. test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
  138. test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
  139. test/new-results/partition-new-simu/fasttree/iclust-2/log +22 -0
  140. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  141. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  142. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  143. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  144. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  145. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  146. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  147. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  148. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  149. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  150. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  151. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  152. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  153. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  154. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  155. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  156. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  157. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  158. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  159. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  160. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  161. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  162. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  163. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  164. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  165. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  166. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  167. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  168. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  169. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  170. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  171. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  172. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  173. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  174. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  175. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  176. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  177. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  178. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  179. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  180. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  181. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  182. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  183. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  184. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  185. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  186. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  187. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  188. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  189. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  190. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  191. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  192. test/new-results/partition-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  193. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  194. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  195. test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  196. test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
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  634. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  635. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  636. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  637. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  638. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  639. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  640. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-66_star_02.csv CHANGED
@@ -1,292 +1,294 @@
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
- 1,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
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75
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76
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77
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78
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79
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80
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81
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82
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83
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84
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85
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86
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87
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88
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89
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90
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91
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92
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93
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94
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95
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96
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97
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98
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99
- 97,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
100
- 98,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
101
- 99,0.14285714285714285,0.093118673237,0.351673214562,0.8571428571428571,6,0.648326785438,0.906881326763,0.0,0,0.0,0.258554541325,0.14285714285714285,1,0.093118673237,0.351673214562,0.0,0,0.0,0.258554541325
102
- 100,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0
103
- 101,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
104
- 102,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
105
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106
- 104,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
107
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108
- 106,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
109
- 107,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
110
- 108,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
111
- 109,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0
112
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113
- 111,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
114
- 112,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
115
- 113,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
116
- 114,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
117
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118
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119
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120
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121
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122
- 120,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
123
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124
- 122,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
125
- 123,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
126
- 124,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
127
- 125,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
128
- 126,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
129
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130
- 128,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
131
- 129,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
132
- 130,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
133
- 131,0.14285714285714285,0.093118673237,0.351673214562,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.8571428571428571,6,0.648326785438,0.906881326763,0.14285714285714285,1,0.093118673237,0.351673214562
134
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135
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136
- 134,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
137
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138
- 136,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
139
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140
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141
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142
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143
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144
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145
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146
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147
- 145,0.2857142857142857,0.182876680964,0.48391587903,0.2857142857142857,2,0.182876680964,0.48391587903,0.7142857142857143,5,0.51608412097,0.817123319036,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
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149
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150
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151
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152
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153
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154
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155
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156
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2
+ 0,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
3
+ 1,0.0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908
4
+ 2,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
5
+ 3,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
6
+ 4,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0
7
+ 5,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
8
+ 6,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908
9
+ 7,0.0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908
10
+ 8,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
11
+ 9,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908
12
+ 10,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0
13
+ 11,0.07142857142857142,0.049202823059,0.200199055967,0.0,0,0.0,0.150996232908,0.07142857142857142,1,0.049202823059,0.200199055967,0.9285714285714286,13,0.799800944033,0.950797176941,0.0,0,0.0,0.150996232908
14
+ 12,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
15
+ 13,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0
16
+ 14,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
17
+ 15,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
18
+ 16,0.0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908
19
+ 17,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
20
+ 18,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0
21
+ 19,0.07142857142857142,0.049202823059,0.200199055967,0.0,0,0.0,0.150996232908,0.9285714285714286,13,0.799800944033,0.950797176941,0.0,0,0.0,0.150996232908,0.07142857142857142,1,0.049202823059,0.200199055967
22
+ 20,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0
23
+ 21,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
24
+ 22,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
25
+ 23,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
26
+ 24,0.0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,0.0,0,0.0,0.150996232908,1.0,14,0.9293769912096106,1.0,0.0,0,0.0,0.150996232908
27
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