partis-bcr 1.0.11.post1.dev1__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 (652) 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.dev3.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/RECORD +652 -125
  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+igl/igl.yaml +1 -0
  635. test/paired/new-results/test/simu/igh.yaml +1 -0
  636. test/paired/new-results/test/simu/igk.yaml +1 -0
  637. test/paired/new-results/test/simu/igl.yaml +1 -0
  638. test/paired/new-results/test/simu/meta.yaml +1 -0
  639. test/paired/new-results/test.log +227 -33
  640. test/test.py +6 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/gctree-run.py +0 -0
  646. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  647. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/parse-output.py +0 -0
  648. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/split-loci.py +0 -0
  649. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/WHEEL +0 -0
  650. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/entry_points.txt +0 -0
  651. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/licenses/COPYING +0 -0
  652. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/top_level.txt +0 -0
{partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/RECORD RENAMED
@@ -25,9 +25,9 @@ bin/lonr.r,sha256=YzAsjyQ-NZ2shOPhzkFFppsgXJEhMTztFA-C6NVyEJ4,44212
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865
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894
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895
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896
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897
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899
+ test/new-results/test/parameters/simu/sw/hmms/IGHD1-20_star_01.yaml,sha256=1XGNilMTcFUqSQQLrimySjNzAwgkUltAVsekx-lmfcc,12832
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+ test/new-results/test/parameters/simu/sw/hmms/IGHD3-16_star_02.yaml,sha256=p5bigmFxdypaboR3bZpeZzYllA_A5fLlQC4bkG-rBeM,25396
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+ test/new-results/test/parameters/simu/sw/hmms/IGHD3-22_star_01.yaml,sha256=bdUBvpHuabehRe9mWab1Dmf3sDq-WfQ9r3F3FIQUQ5I,21291
902
+ test/new-results/test/parameters/simu/sw/hmms/IGHD6-13_star_01.yaml,sha256=-5yIjNtkfO0en3nN5KPaN_cfIUFL_S-kW1vul0aXdfk,15352
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904
+ test/new-results/test/parameters/simu/sw/hmms/IGHJ1_star_01.yaml,sha256=GyaCoyKZqdj6Y3NxeQMDxTfecjiWSRiUFCrobq2oHgQ,24169
905
+ test/new-results/test/parameters/simu/sw/hmms/IGHJ4_star_02.yaml,sha256=daEZ8sBg1QDnXNu2pUkl-6rjYW1NweOHhEENRCYoXkk,22405
906
+ test/new-results/test/parameters/simu/sw/hmms/IGHJ6_star_02.yaml,sha256=at7AGRfVop9R4T6p2CThtweiunwhmkSjWOv9rdFicHw,30730
907
+ test/new-results/test/parameters/simu/sw/hmms/IGHV1-18_star_01.yaml,sha256=3R9t3lHMQYEnALWi4ZEO52aI3ivXsaVr2RWkk_PH4VE,105925
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+ test/new-results/test/parameters/simu/sw/hmms/IGHV3-23_star_01.yaml,sha256=q2Lf3t0fO7F91q0Cba76HOz149bwMAXjQ2xuT0yMIuI,105405
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+ test/new-results/test/parameters/simu/sw/hmms/IGHV3-66_star_02.yaml,sha256=VwiYswrRUiBcFp9Hob3wc2g-ClRWyDOONpgBTisGdL4,99833
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+ test/new-results/test/parameters/simu/sw/hmms/IGHV3-7_star_05.yaml,sha256=mpZ6qNLzzP5hKEGiGFC0scRxRkjcSK_-_V9ybeL6OCM,103495
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+ test/new-results/test/parameters/simu/sw/hmms/IGHV4-4_star_09.yaml,sha256=atoeu1qDs6F-p86b2AxUCdkml2ISkx66CoOckHeAXog,103232
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+ test/new-results/test/parameters/simu/sw/hmms/IGHV4-61_star_01.yaml,sha256=J6o77081GzjZcgMR8hN6kvPzRSLUYOMklXbpoDTcVDw,101718
913
+ test/new-results/test/parameters/simu/sw/hmms/IGHV5-51_star_01.yaml,sha256=Yffn4kuvSBsjKMpVjkbGkoMaUV2gxenMB9UhnwAMeW0,104913
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHD1-20_star_01.csv,sha256=Vw0UbtEmrlYjjgBKCMERteu-WtDIQkO2EihZfdqkKlU,1179
915
+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-16_star_02.csv,sha256=aFOFT0TCkp7NJgB5FWblIRqgrpLVwTL4zA8wRZ3fE4M,3935
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-22_star_01.csv,sha256=qSsicAv6b3ZwyJqXfbW74akt7g8JPk8_ktlUUSptoKs,4263
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-13_star_01.csv,sha256=lbHygnE7ETSq_w7xq0VWNHO2BshyGj2_j67GXTFgW78,2956
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-19_star_01.csv,sha256=aYBYSGRcfWJeJE2SgyYpdb4JITAj_Nj47qtLBzBiO64,2617
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ1_star_01.csv,sha256=Qqrvy8SpNNMwucEG8ZpDBMpPOznFTDS38FbC3LpfGak,6696
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ4_star_02.csv,sha256=vFbWPWYhY1tfDlhXYqujIDBECowy7XwwvNcUiOoKZFQ,6746
454
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- test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv,sha256=L2u0w3IWDJKOshqCT6St6SxKKPAjq6JbY0JDH9uBMls,39711
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHV1-18_star_01.csv,sha256=qWQvD-ltkpm5pNBo6oy9HCx45zn6MPuwV6F0EhKn_CQ,39176
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-23_star_01.csv,sha256=iggcygo5zN-Wevze_vahlPZKGt7Kn2RTJ6NIMMIGq2Q,39100
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv,sha256=NuxSOkAlYSTLH1pYiglewkxG17C6AudeiodkogUY03o,41148
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-4_star_09.csv,sha256=_2s4lvITWRfamkX32TTOzhCd_tCF7qOnY1LJ5y1jAx0,38320
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-61_star_01.csv,sha256=kONUU7EHhpBiHqSGDoWdTA5zBjaMYZDo385OHxsD5_w,40111
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+ test/new-results/test/parameters/simu/sw/mute-freqs/IGHV5-51_star_01.csv,sha256=0BOZU7pYns4oh593bGeq2V-qPaLAdH33RodQUnwDmlo,38980
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+ test/new-results/test/parameters/simu/true/all-mean-mute-freqs.csv,sha256=0pdxyoFEXH3_eow_rK7arPkKCuj5gluaUgPnlOzJ0v4,771
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+ test/new-results/test/parameters/simu/true/all-mean-n-muted.csv,sha256=q4lxyZKrQ9rXEttFW98beQBkstUDvzZhNlSwTihKwiU,2420
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+ test/new-results/test/parameters/simu/true/all-probs.csv,sha256=hY2LPP1S13b1EqphO0z4SSGDyERj6JCdMm3hVcKwTGM,679
932
+ test/new-results/test/parameters/simu/true/cluster_size.csv,sha256=1aSbRzyfEI9p3sFsY0Siwc-xevi6Px9jMGpAs4Aedrc,50
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+ test/new-results/test/parameters/simu/true/d-mean-mute-freqs.csv,sha256=UahkZJ9Qzdq4AgtaJek2Ix4zRc4fkZiqfIdXX9SEJ60,839
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+ test/new-results/test/parameters/simu/true/d-mean-n-muted.csv,sha256=3Lkb-ACXnUu1jn1PYLsdPA32xR4wC-Q6MVXJTszM9lg,239
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+ test/new-results/test/parameters/simu/true/d_gene-d_3p_del-probs.csv,sha256=mpMljUR2axM8L6ixhCMSOBQvEHip6gsmvhuca9jhzgU,158
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+ test/new-results/test/parameters/simu/true/d_gene-d_5p_del-probs.csv,sha256=MMmhzJV5yXsGk_rt8z_HRSa4Nhzn3vV-s8GEGEp8sso,175
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+ test/new-results/test/parameters/simu/true/d_gene-probs.csv,sha256=UJ8DnHJm7hFYc0e-7OO9zBRYjIN4yeJ57SeX2IAcms8,103
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+ test/new-results/test/parameters/simu/true/d_gene-vd_insertion-probs.csv,sha256=pTSQcrIo99xjdS9HJSqoRZ2PQO6acaFEnkMXROBk_C0,181
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+ test/new-results/test/parameters/simu/true/dj_insertion_content.csv,sha256=WHqH0mjXBmtPUJhbgqHDuYIb35-WWeM33CqQPaQPKfY,51
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+ test/new-results/test/parameters/simu/true/fv_insertion-probs.csv,sha256=y05g9xpId6ehhoFDZ1yoEljOp1OoqKDrjy7UlVuv7PI,26
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+ test/new-results/test/parameters/simu/true/j-mean-mute-freqs.csv,sha256=kMbmokeNapXdhTxTHGMYi3qTzvKFWq-GbtWzaQWdEl0,770
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+ test/new-results/test/parameters/simu/true/j-mean-n-muted.csv,sha256=f4AVgobW2wOfrnZPSdh15Iy-BnN1iI9J4nP3OQKCBrY,415
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+ test/new-results/test/parameters/simu/true/j_gene-dj_insertion-probs.csv,sha256=nMU9eRj_43tq1ogwBJGcQeqJDTGUSEnH8vI1I9HjF3M,112
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+ test/new-results/test/parameters/simu/true/j_gene-j_3p_del-probs.csv,sha256=IP0jTfQI6B-CK3zClQGvWMfhqm-zc3aU8cETGuQopmI,65
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+ test/new-results/test/parameters/simu/true/j_gene-j_5p_del-probs.csv,sha256=XxREd24V4MAqn0zhwJEI_lmyeChgbwUYQYG9xsaPiF8,137
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+ test/new-results/test/parameters/simu/true/j_gene-probs.csv,sha256=qg5ZdxeKFfiZ9piaIEtJlpGZC0O7BHbyuKzCQhNV9a8,50
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+ test/new-results/test/parameters/simu/true/jf_insertion-probs.csv,sha256=OhShrBTyasDthMLCsDxkrMj3pHoAkzVTPVxoVc39puQ,26
948
+ test/new-results/test/parameters/simu/true/seq_content.csv,sha256=LUX5kr1RY-F5XQhnK7ZndM8cdnYaz_R66xTUnwAkBlE,51
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+ test/new-results/test/parameters/simu/true/v-mean-mute-freqs.csv,sha256=G0ooefygl__ryhmyyRgDb3c2NREYOkC7fWVHbCezbn4,771
950
+ test/new-results/test/parameters/simu/true/v-mean-n-muted.csv,sha256=2K3dN6XnTGHc1n6QWaVI4J_wfTON-pKMH9l3qJyjse4,1968
951
+ test/new-results/test/parameters/simu/true/v_gene-probs.csv,sha256=NXBVg94oMfmIpdVh68B5UKgXELNbFc0OelrYpR6S6ZQ,117
952
+ test/new-results/test/parameters/simu/true/v_gene-v_3p_del-probs.csv,sha256=zCIRZ1SlvG19X6MGS7wYfzJlbaENfrnWRDgxgq-VnWk,157
953
+ test/new-results/test/parameters/simu/true/v_gene-v_5p_del-probs.csv,sha256=YuRwBSDaskKmoYMCu8ZXAEW7LNXfvHmHS7lhPk5JilI,140
954
+ test/new-results/test/parameters/simu/true/vd_insertion_content.csv,sha256=eS1NA66q7A8orZZer1rRDySSX3bNcHLxX3mlKV9wF0o,51
955
+ test/new-results/test/parameters/simu/true/germline-sets/igh/extras.csv,sha256=36Sev7hCZRR-lcdnr9p4M--oDkqr_p2j0vGangs-7FA,246
956
+ test/new-results/test/parameters/simu/true/germline-sets/igh/ighd.fasta,sha256=KEJLTTD0_9WPqceiQAB2_LJXKwUshvC7LlHZrs1KPbI,228
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+ test/new-results/test/parameters/simu/true/germline-sets/igh/ighj.fasta,sha256=4UWQNkDWhOFeKG36_460WRbmJ_5BKsDi7ibAa1uhATI,196
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+ test/new-results/test/parameters/simu/true/germline-sets/igh/ighv.fasta,sha256=xtHU6LKeyp16GSsxM749mqAy4hfAs-eimWjvss8ogy0,2165
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHD1-20_star_01.csv,sha256=ANvC4GAbFcAqIW7f0DQcWbq2qZK_ZvlIAIiRiGr0W9E,1048
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHD3-16_star_02.csv,sha256=aFOFT0TCkp7NJgB5FWblIRqgrpLVwTL4zA8wRZ3fE4M,3935
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHD3-22_star_01.csv,sha256=qSsicAv6b3ZwyJqXfbW74akt7g8JPk8_ktlUUSptoKs,4263
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHD6-13_star_01.csv,sha256=qQ-ZaUHWJXyxz5AeyAU6oJg6R2X1dGiiA8HYkAGppV8,3090
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHD6-19_star_01.csv,sha256=TODqY-bHf6qXTM8qGMehBrGTtNBxWSCRkCncFyzUdck,2879
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHD6-6_star_01.csv,sha256=Si4QG-npAa1ad2NuyDQwOCdb3Y-YVQTMdsqE4UBrIJI,1700
965
+ test/new-results/test/parameters/simu/true/mute-freqs/IGHJ1_star_01.csv,sha256=uLdRseO-LvPJJAYj4aBNyDJuRWLJew9g4UAvrx4uJwY,6655
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHJ4_star_02.csv,sha256=KfLR2MD8pOUO9mN1cTFDHex0VEsOad8PPg1d_XVE8F8,6116
967
+ test/new-results/test/parameters/simu/true/mute-freqs/IGHJ6_star_02.csv,sha256=-nvF_Re3o29DhELGSHCanf8UF4894aGmLvaDahgjIHo,6238
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHV1-18_star_01.csv,sha256=qWQvD-ltkpm5pNBo6oy9HCx45zn6MPuwV6F0EhKn_CQ,39176
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHV3-23_star_01.csv,sha256=iggcygo5zN-Wevze_vahlPZKGt7Kn2RTJ6NIMMIGq2Q,39100
970
+ test/new-results/test/parameters/simu/true/mute-freqs/IGHV3-66_star_02.csv,sha256=NuxSOkAlYSTLH1pYiglewkxG17C6AudeiodkogUY03o,41148
971
+ test/new-results/test/parameters/simu/true/mute-freqs/IGHV3-7_star_05.csv,sha256=Ve6Y1IAOpf0ls0fwDtz7KMoMxrGtH2RadkomESpABR8,39704
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-4_star_09.csv,sha256=_2s4lvITWRfamkX32TTOzhCd_tCF7qOnY1LJ5y1jAx0,38320
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-61_star_01.csv,sha256=kONUU7EHhpBiHqSGDoWdTA5zBjaMYZDo385OHxsD5_w,40111
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+ test/new-results/test/parameters/simu/true/mute-freqs/IGHV5-51_star_01.csv,sha256=0BOZU7pYns4oh593bGeq2V-qPaLAdH33RodQUnwDmlo,38980
457
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  test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv,sha256=pPLqsoWr7MChKJCeXfFDEo6JS4IG21TgmLzoMi5-vdQ,12593
458
- test/paired/new-results/run-times.csv,sha256=MUp5bJZEWXEcu0x1YAafIOX81poLlpSg6apMsmM9UeM,193
459
- test/paired/new-results/test.log,sha256=16WvLbC2MIwfXIxQ_bbIMcZlAGhiRowvZChYrOWvA-g,70718
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+ test/paired/new-results/run-times.csv,sha256=He9aZWw2BudfEJG-YYRvpA6ccqki6uZBNla84f2OxKQ,208
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+ test/paired/new-results/test.log,sha256=7QbWzBA7yDYtMZOWbUOi70EgH_TQcK3DB7HmQAgpfjA,85873
460
978
  test/paired/new-results/partition-new-simu/partition-igh.yaml,sha256=qelM_0rtDDwpLWl6_ItvkrXioZ9MI6VMiLPMf6tcbIs,71140
461
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  test/paired/new-results/partition-new-simu/partition-igk.yaml,sha256=9iTcIjgyiVsoADqym9El14fwDT4nU_xu2mWy_UeVHSA,46688
462
980
  test/paired/new-results/partition-new-simu/partition-igl.yaml,sha256=XdV7rr3fQJPi3-5NvCxhHI4k5huOja8zxdI9XHWatMQ,23871
@@ -477,7 +995,7 @@ test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa,sha25
477
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  test/paired/new-results/partition-new-simu/fasttree/iclust-1/log,sha256=ou_xxqXaZukRTI1w7eqlqmq0-kTNCasOjtqgC2mJ85A,1535
478
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  test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out,sha256=8iAGmWkl8Cw1An8YerCdGi3dYbBCqM03erljLmfZch0,234
479
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  test/paired/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa,sha256=XvNc2wDAuQR3Z7JnQF3QYnPxfYpQH3KzP__OfQymTcw,4434
480
- test/paired/new-results/partition-new-simu/fasttree/iclust-2/log,sha256=25KZIP4HeKCMxU4DesdGXYNygTysU6ZT4VMYzmWlgDA,1535
998
+ test/paired/new-results/partition-new-simu/fasttree/iclust-2/log,sha256=0B3jw_M5grPDVLkbVo0jzDZr40PZciuapueNAhQD9DU,1535
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  test/paired/new-results/partition-new-simu/igh+igk/partition-igh-selection-metrics.yaml,sha256=qnyJc6r4fEij37iP8yKvwXdXa6oz1GlprIABjBvEac4,5954
482
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  test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml,sha256=TvdmgfDmKq9FTXSZ8WvsP85OsORW3qB2hqMbGZG7_Ss,43157
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  test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metrics.yaml,sha256=1cTAXjSz2J7eW7WYV9a1HOnBArqlO66a9M3HQiMTuA0,4635
@@ -487,7 +1005,7 @@ test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust
487
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  test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log,sha256=vO7VmqU3ovUHv5eeBQjBL4_OkUPmSrkzRJA-ygBuRy0,1693
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  test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out,sha256=R_clhMra-ApsWz9L57q5eee5ouu2TRfhss6AEPherxA,217
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  test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/input-seqs.fa,sha256=_AA1cnLEZd2n60CZ_FRSeUID4yggqfQyBXBbRa0ke5w,2723
490
- test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log,sha256=5UepSdUakrSNr48Z2u1gFSlD0TP0qsR_oAUlgFsnkHE,1692
1008
+ test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log,sha256=h81UNPsuHrMD0xu7yvQLELsttjwQCnlV8MB3joqjNVk,1692
491
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  test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/fasttree.out,sha256=4BPvTBrBWb0QNzUIgOAifNN5zlQn2pwLeHyXL62KKAY,166
492
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  test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/input-seqs.fa,sha256=xmghMTcWRSKgyfKU2rnLHgIF5uDeVXOkQH2xOPKxo-o,2825
493
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  test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log,sha256=WRAXrrNjPEfivA5dkHsOQFrvq-mnZ0O5JfZHg8SxcBY,1693
@@ -511,34 +1029,34 @@ test/paired/new-results/partition-new-simu/single-chain/partition-igh.yaml,sha25
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  test/paired/new-results/partition-new-simu/single-chain/partition-igk.yaml,sha256=o-a0agImpMjjo32u7TaIrHbTW_RXJPkHXD8znweeT8Y,38067
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  test/paired/new-results/partition-new-simu/single-chain/partition-igl.yaml,sha256=vEjx11N8dkIpx00_h5_qM4dis3254HeEsza7qkTre4I,18883
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+ test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=m88OP5rXm3g__cOs_6ZcwqiVFCkRhol7u99Wwhc8qTE,9771
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@@ -731,7 +1249,7 @@ test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-
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@@ -755,7 +1273,7 @@ test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml,sha256=ZUaFW7
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- test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=97DGQAzHTQSyc8NnqqTb5H0XZsMJu1xXTBfFwRZk_Ys,24021
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+ test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=6ZAuNzq2itZ62ykhF5qEEXd8-BnRniTZapLYXeAZWOA,24021
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@@ -1106,7 +1624,7 @@ test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml,sha256=J_IVfe
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- test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=FQ3rOWkdjCN5w5zfNSYXVtqlJrrqhEUhj_htBaYyJGo,23969
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+ test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=b_m_IA9lQA-u5TEUzDi-ukYVWFybvjFZ4Rbaq_0GZhQ,23969
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@@ -1475,7 +1993,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partiti
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1996
+ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=9LfVQ3Iz9E0AdSwytCAzoAMpxXdIhkYmPwVnVnrbEp8,140753
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  test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/all-mean-mute-freqs.csv,sha256=LPJkL33RJZwT1nbvv80p_1r5J6pSyejnAb1rxjB5eU8,912
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@@ -1509,7 +2027,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/
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  test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV3-33_star_01.yaml,sha256=FU4oDYBlqRgZwlQrbG23AEZneBh-icKPaswTKnXojUI,103996
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- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=nDcz98p6nt7EWQwwXyl9zs4Keu167vPkO93844wxHcU,78754
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+ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=v8V9bQranwPJOnhsniI0m3WPEM7qNFWtc69kFY49UwI,78754
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  test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/all-mean-mute-freqs.csv,sha256=yR5AuVGrcUAOe72bT-nEJap_zn3AwCpaXSrFGELbDyA,740
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@@ -1528,7 +2046,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/
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- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=GsxUJUspmQpWaqTRFOqItdOwBT9C_5yZaut5vDTz9s8,44439
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+ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=Q5evTls-3iK3wEtsKpPf5fiDcWboLUYpTtwD9y8KteI,44439
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@@ -2540,6 +3058,15 @@ test/paired/new-results/test/parameters/simu/igl/true/mute-freqs/IGLJ3_star_02.c
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  test/paired/new-results/test/parameters/simu/igl/true/mute-freqs/IGLV2-23_star_02.csv,sha256=NNCfbwB78nBRyZxpP6CerXnVqbmxjZYupYkdYMYsvL4,38044
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+ test/paired/new-results/test/simu/all-seqs.fa,sha256=SYRQHETSU0POoVxhBNbr7SjmQZTYHs73g2qickY6Rxg,40997
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+ test/paired/new-results/test/simu/igh.yaml,sha256=WqKR5dQ8r96mCKg2IRF81QOi0oW-A3vCP_qn55RM9Jg,60026
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+ test/paired/new-results/test/simu/igk.yaml,sha256=TWd2n2mbB3TbkcE7VIY-eSkfe8W302ups2Sey9JlIME,38712
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+ test/paired/new-results/test/simu/igl.yaml,sha256=BQl2aSLIJSZ527drIXHfREzHMfUdV9vS9MGPFCwMddg,20571
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+ test/paired/new-results/test/simu/meta.yaml,sha256=K2YrRqiQigNRUwo5HbzUgeS-YjZ482qiP9TA4W4wAeQ,8955
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+ test/paired/new-results/test/simu/igh+igk/igh.yaml,sha256=fwJUnfouRe2mvjkfrc7R61xDRWrlLoYvlceXQhCGIok,37784
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+ test/paired/new-results/test/simu/igh+igk/igk.yaml,sha256=TWd2n2mbB3TbkcE7VIY-eSkfe8W302ups2Sey9JlIME,38712
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+ test/paired/new-results/test/simu/igh+igl/igh.yaml,sha256=RGmmNyiQ9-UDyOY2_fnDzpo9kBcMR3EpOZ0_RMoE1yk,31490
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+ test/paired/new-results/test/simu/igh+igl/igl.yaml,sha256=BQl2aSLIJSZ527drIXHfREzHMfUdV9vS9MGPFCwMddg,20571
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  test/paired/ref-results/get-selection-metrics-new-simu-chosen-abs.csv,sha256=pPLqsoWr7MChKJCeXfFDEo6JS4IG21TgmLzoMi5-vdQ,12593
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  test/paired/ref-results/run-times.csv,sha256=hFA6Pz-Qw3UzqYiKjObhgKAYIK9g0PnNqjGy2RCjOQQ,238
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  test/paired/ref-results/test.log,sha256=Ju_Oo1TSl2_R9KQvtFuHdYxJGjL9WbBtFy2SpqT9Tlg,85256
@@ -7898,8 +8425,8 @@ test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV4-NL1_star_01.csv
7898
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  test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV5-10-1_star_01.csv,sha256=S075HCAZnbZpAMsXeLMmMXEGVHFs_Euk1XujtFQ46y4,41974
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  test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV5-51_star_01.csv,sha256=QJGyDRqD2JezXsuMbNNXGSCM-kjaN2h4QGpgsaqTqXQ,57817
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  test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV7-4-1_star_02.csv,sha256=k5KeCR5Qa6iEF0IEHR63DDdJStqAjcZxgZOUbKDFNaY,39977
7901
- partis_bcr-1.0.11.post1.dev1.dist-info/METADATA,sha256=6ShzvolO4EwZl-P13LVatUIlWpy837twI_X-taZO3fU,5019
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- partis_bcr-1.0.11.post1.dev1.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
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- partis_bcr-1.0.11.post1.dev1.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
7904
- partis_bcr-1.0.11.post1.dev1.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
7905
- partis_bcr-1.0.11.post1.dev1.dist-info/RECORD,,
8428
+ partis_bcr-1.0.11.post1.dev3.dist-info/METADATA,sha256=hVIsGVEKaXzw2a3-qkeSsEhwaKo3LZeuXAntvK14MrE,5019
8429
+ partis_bcr-1.0.11.post1.dev3.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
8430
+ partis_bcr-1.0.11.post1.dev3.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
8431
+ partis_bcr-1.0.11.post1.dev3.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
8432
+ partis_bcr-1.0.11.post1.dev3.dist-info/RECORD,,