partis-bcr 1.0.11__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 (644) hide show
  1. bin/partis +1 -1
  2. bin/partis-test.py +6 -0
  3. bin/partis.py +1 -1
  4. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +644 -126
  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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  632. test/trees.nwk +100 -0
  633. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  634. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  635. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  636. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  637. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  638. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  639. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  640. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  641. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  642. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  643. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  644. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/hmm/hmms/IGHD3-22_star_01.yaml ADDED
@@ -0,0 +1,744 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
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+ gene_prob: 0.2222222222222222
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+ overall_mute_freq: 0.012499999999999999
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+ per_gene_mute_freq: 0.11017777849300642
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+ name: IGHD3-22_star_01
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+ states:
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+ - !!python/object:python.hmmwriter.State
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+ emissions: null
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+ extras: {}
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+ name: init
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+ transitions:
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+ IGHD3-22_star_01_0: 0.18947368421052632
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+ IGHD3-22_star_01_1: 0.02368421052631579
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+ IGHD3-22_star_01_10: 0.02368421052631579
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+ IGHD3-22_star_01_11: 0.02368421052631579
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+ IGHD3-22_star_01_12: 0.02368421052631579
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+ IGHD3-22_star_01_13: 0.02368421052631579
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+ IGHD3-22_star_01_14: 0.02368421052631579
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+ IGHD3-22_star_01_15: 0.02368421052631579
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+ IGHD3-22_star_01_16: 0.02368421052631579
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+ IGHD3-22_star_01_17: 0.02368421052631579
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+ IGHD3-22_star_01_18: 0.02368421052631579
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+ IGHD3-22_star_01_19: 0.02368421052631579
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+ IGHD3-22_star_01_2: 0.02368421052631579
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+ IGHD3-22_star_01_20: 0.02368421052631579
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+ IGHD3-22_star_01_21: 0.02368421052631579
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+ IGHD3-22_star_01_22: 0.02368421052631579
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+ IGHD3-22_star_01_23: 0.02368421052631579
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+ IGHD3-22_star_01_24: 0.02368421052631579
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+ IGHD3-22_star_01_25: 0.02368421052631579
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+ IGHD3-22_star_01_26: 0.02368421052631579
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+ IGHD3-22_star_01_27: 0.02368421052631579
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+ IGHD3-22_star_01_28: 0.02368421052631579
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+ IGHD3-22_star_01_29: 0.02368421052631579
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+ IGHD3-22_star_01_3: 0.02368421052631579
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+ IGHD3-22_star_01_30: 0.02368421052631579
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+ IGHD3-22_star_01_4: 0.02368421052631579
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+ IGHD3-22_star_01_5: 0.02368421052631579
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+ IGHD3-22_star_01_6: 0.02368421052631579
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+ IGHD3-22_star_01_7: 0.02368421052631579
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+ IGHD3-22_star_01_8: 0.02368421052631579
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+ IGHD3-22_star_01_9: 0.02368421052631579
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+ insert_left_A: 0.011347517730496451
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+ insert_left_C: 0.045390070921985805
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+ insert_left_G: 0.016312056737588652
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+ insert_left_T: 0.026950354609929072
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ A: 0.8898222215069935
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+ C: 0.036725926164335475
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+ T: 0.036725926164335475
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: A
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+ name: insert_left_A
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+ transitions:
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+ IGHD3-22_star_01_0: 0.18947368421052632
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+ IGHD3-22_star_01_1: 0.02368421052631579
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+ IGHD3-22_star_01_10: 0.02368421052631579
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+ IGHD3-22_star_01_11: 0.02368421052631579
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+ IGHD3-22_star_01_12: 0.02368421052631579
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+ IGHD3-22_star_01_13: 0.02368421052631579
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+ IGHD3-22_star_01_14: 0.02368421052631579
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+ IGHD3-22_star_01_15: 0.02368421052631579
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+ IGHD3-22_star_01_16: 0.02368421052631579
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+ IGHD3-22_star_01_17: 0.02368421052631579
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+ IGHD3-22_star_01_18: 0.02368421052631579
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+ IGHD3-22_star_01_2: 0.02368421052631579
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+ IGHD3-22_star_01_20: 0.02368421052631579
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+ IGHD3-22_star_01_21: 0.02368421052631579
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+ IGHD3-22_star_01_22: 0.02368421052631579
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+ IGHD3-22_star_01_23: 0.02368421052631579
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+ IGHD3-22_star_01_24: 0.02368421052631579
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+ IGHD3-22_star_01_25: 0.02368421052631579
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+ IGHD3-22_star_01_26: 0.02368421052631579
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+ IGHD3-22_star_01_27: 0.02368421052631579
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+ IGHD3-22_star_01_28: 0.02368421052631579
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+ IGHD3-22_star_01_29: 0.02368421052631579
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+ IGHD3-22_star_01_30: 0.02368421052631579
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+ IGHD3-22_star_01_4: 0.02368421052631579
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+ IGHD3-22_star_01_6: 0.02368421052631579
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+ IGHD3-22_star_01_7: 0.02368421052631579
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+ IGHD3-22_star_01_8: 0.02368421052631579
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+ IGHD3-22_star_01_9: 0.02368421052631579
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+ insert_left_A: 0.011347517730496451
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+ insert_left_C: 0.045390070921985805
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+ insert_left_G: 0.016312056737588652
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+ insert_left_T: 0.026950354609929072
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: C
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+ name: insert_left_C
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+ transitions:
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+ IGHD3-22_star_01_0: 0.18947368421052632
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+ IGHD3-22_star_01_14: 0.02368421052631579
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+ IGHD3-22_star_01_15: 0.02368421052631579
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+ IGHD3-22_star_01_16: 0.02368421052631579
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+ IGHD3-22_star_01_17: 0.02368421052631579
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+ IGHD3-22_star_01_18: 0.02368421052631579
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+ IGHD3-22_star_01_19: 0.02368421052631579
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+ IGHD3-22_star_01_2: 0.02368421052631579
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+ IGHD3-22_star_01_20: 0.02368421052631579
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+ IGHD3-22_star_01_21: 0.02368421052631579
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+ IGHD3-22_star_01_22: 0.02368421052631579
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+ IGHD3-22_star_01_23: 0.02368421052631579
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+ IGHD3-22_star_01_24: 0.02368421052631579
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+ IGHD3-22_star_01_25: 0.02368421052631579
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+ IGHD3-22_star_01_26: 0.02368421052631579
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+ IGHD3-22_star_01_27: 0.02368421052631579
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+ IGHD3-22_star_01_28: 0.02368421052631579
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+ IGHD3-22_star_01_29: 0.02368421052631579
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+ IGHD3-22_star_01_3: 0.02368421052631579
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+ IGHD3-22_star_01_30: 0.02368421052631579
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+ IGHD3-22_star_01_4: 0.02368421052631579
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+ IGHD3-22_star_01_5: 0.02368421052631579
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+ IGHD3-22_star_01_6: 0.02368421052631579
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+ IGHD3-22_star_01_7: 0.02368421052631579
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+ IGHD3-22_star_01_8: 0.02368421052631579
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+ IGHD3-22_star_01_9: 0.02368421052631579
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+ insert_left_A: 0.011347517730496451
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+ insert_left_C: 0.045390070921985805
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+ insert_left_G: 0.016312056737588652
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+ insert_left_T: 0.026950354609929072
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ extras:
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+ germline: G
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+ name: insert_left_G
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+ transitions:
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+ IGHD3-22_star_01_0: 0.18947368421052632
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+ IGHD3-22_star_01_1: 0.02368421052631579
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+ IGHD3-22_star_01_10: 0.02368421052631579
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+ IGHD3-22_star_01_11: 0.02368421052631579
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+ IGHD3-22_star_01_14: 0.02368421052631579
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+ IGHD3-22_star_01_15: 0.02368421052631579
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+ IGHD3-22_star_01_16: 0.02368421052631579
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+ IGHD3-22_star_01_17: 0.02368421052631579
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+ IGHD3-22_star_01_18: 0.02368421052631579
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+ IGHD3-22_star_01_19: 0.02368421052631579
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+ IGHD3-22_star_01_2: 0.02368421052631579
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+ IGHD3-22_star_01_20: 0.02368421052631579
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+ IGHD3-22_star_01_21: 0.02368421052631579
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+ IGHD3-22_star_01_22: 0.02368421052631579
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+ IGHD3-22_star_01_23: 0.02368421052631579
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+ IGHD3-22_star_01_24: 0.02368421052631579
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+ IGHD3-22_star_01_25: 0.02368421052631579
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+ IGHD3-22_star_01_26: 0.02368421052631579
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+ IGHD3-22_star_01_27: 0.02368421052631579
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+ IGHD3-22_star_01_28: 0.02368421052631579
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+ IGHD3-22_star_01_29: 0.02368421052631579
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+ IGHD3-22_star_01_3: 0.02368421052631579
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+ IGHD3-22_star_01_30: 0.02368421052631579
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+ IGHD3-22_star_01_4: 0.02368421052631579
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+ IGHD3-22_star_01_5: 0.02368421052631579
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+ IGHD3-22_star_01_6: 0.02368421052631579
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+ IGHD3-22_star_01_7: 0.02368421052631579
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+ IGHD3-22_star_01_8: 0.02368421052631579
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+ IGHD3-22_star_01_9: 0.02368421052631579
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+ insert_left_A: 0.011347517730496451
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+ insert_left_C: 0.045390070921985805
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+ insert_left_G: 0.016312056737588652
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+ insert_left_T: 0.026950354609929072
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: insert_left_T
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+ transitions:
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+ IGHD3-22_star_01_0: 0.18947368421052632
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+ IGHD3-22_star_01_8: 0.02368421052631579
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+ IGHD3-22_star_01_9: 0.02368421052631579
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+ insert_left_T: 0.026950354609929072
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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386
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388
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389
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390
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391
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392
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393
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394
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395
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396
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397
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398
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399
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400
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401
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402
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403
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404
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405
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406
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407
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408
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409
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410
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411
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412
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413
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414
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415
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416
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417
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418
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419
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420
+ - !!python/object:python.hmmwriter.State
421
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422
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423
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424
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425
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426
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427
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428
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429
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430
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431
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432
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433
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434
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435
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436
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437
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438
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439
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440
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441
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442
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443
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444
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445
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446
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447
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448
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449
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450
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451
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452
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453
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454
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455
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456
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457
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458
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459
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460
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461
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462
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463
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464
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465
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466
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467
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468
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469
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470
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471
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472
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473
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474
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475
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476
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477
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478
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479
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480
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481
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482
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483
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484
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485
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486
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487
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488
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489
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490
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491
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492
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493
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494
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495
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496
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497
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498
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499
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500
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501
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502
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503
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504
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505
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506
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507
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508
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509
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510
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511
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512
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513
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514
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515
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516
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517
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518
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519
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520
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521
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522
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523
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524
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525
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526
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527
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528
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529
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530
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531
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532
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533
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534
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535
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536
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537
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538
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539
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540
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541
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542
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543
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544
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545
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546
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547
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548
+ - !!python/object:python.hmmwriter.State
549
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550
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551
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552
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553
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554
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555
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556
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557
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558
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559
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560
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561
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562
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563
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564
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565
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566
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567
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568
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569
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570
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571
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572
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573
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574
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575
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576
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577
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578
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579
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580
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581
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582
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583
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584
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585
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586
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587
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588
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589
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590
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591
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592
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593
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594
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595
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596
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597
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598
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600
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601
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602
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603
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604
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605
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606
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607
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608
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609
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610
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611
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612
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613
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614
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615
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616
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617
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618
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619
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620
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621
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622
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623
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624
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625
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626
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627
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628
+ - !!python/object:python.hmmwriter.State
629
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630
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632
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634
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635
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636
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638
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639
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640
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641
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642
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643
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644
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645
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646
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648
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649
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650
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651
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652
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654
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655
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656
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657
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658
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659
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660
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661
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662
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664
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665
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667
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668
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670
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671
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672
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673
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674
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675
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676
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677
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680
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681
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683
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684
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685
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686
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687
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688
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689
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690
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691
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692
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693
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694
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696
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700
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701
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702
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703
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704
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705
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706
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707
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708
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709
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712
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715
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716
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718
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719
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720
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721
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723
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724
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725
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734
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735
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736
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737
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739
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742
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744
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