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/data/hmm/hmms/IGHV3-66_star_02.yaml ADDED
@@ -0,0 +1,4439 @@
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+ !!python/object:python.hmmwriter.HMM
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+ extras:
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+ emissions: null
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+ name: init
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+ insert_left_N: 0.6666666666666667
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+ transitions:
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+ IGHV3-66_star_02_0: 0.33333333333333326
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+ insert_left_N: 0.6666666666666667
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+ IGHV3-66_star_02_1: 1.0
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1142
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1157
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1172
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1175
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1177
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1187
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1196
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1199
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1200
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1217
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1229
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1232
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1235
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1244
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1247
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1262
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1265
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1274
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1277
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1289
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1292
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1301
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1306
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1307
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1321
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1322
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1337
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1349
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1351
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1352
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1361
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1364
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1365
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1366
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1367
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1376
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1378
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1379
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1381
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1382
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1394
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1396
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1397
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1406
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1411
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1412
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1427
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1442
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1457
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1471
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1472
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1487
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1517
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1532
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1547
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1689
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1690
+ ambiguous_char: N
1691
+ ambiguous_emission_prob: 0.25
1692
+ germline: C
1693
+ name: IGHV3-66_star_02_110
1694
+ transitions:
1695
+ IGHV3-66_star_02_111: 1.0
1696
+ - !!python/object:python.hmmwriter.State
1697
+ emissions:
1698
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1699
+ A: 0.036749014910624996
1700
+ C: 0.889752955268125
1701
+ G: 0.036749014910624996
1702
+ T: 0.036749014910624996
1703
+ track: nukes
1704
+ extras:
1705
+ ambiguous_char: N
1706
+ ambiguous_emission_prob: 0.25
1707
+ germline: C
1708
+ name: IGHV3-66_star_02_111
1709
+ transitions:
1710
+ IGHV3-66_star_02_112: 1.0
1711
+ - !!python/object:python.hmmwriter.State
1712
+ emissions:
1713
+ probs:
1714
+ A: 0.03833333333333333
1715
+ C: 0.03833333333333333
1716
+ G: 0.885
1717
+ T: 0.03833333333333333
1718
+ track: nukes
1719
+ extras:
1720
+ ambiguous_char: N
1721
+ ambiguous_emission_prob: 0.25
1722
+ germline: G
1723
+ name: IGHV3-66_star_02_112
1724
+ transitions:
1725
+ IGHV3-66_star_02_113: 1.0
1726
+ - !!python/object:python.hmmwriter.State
1727
+ emissions:
1728
+ probs:
1729
+ A: 0.036749014910624996
1730
+ C: 0.889752955268125
1731
+ G: 0.036749014910624996
1732
+ T: 0.036749014910624996
1733
+ track: nukes
1734
+ extras:
1735
+ ambiguous_char: N
1736
+ ambiguous_emission_prob: 0.25
1737
+ germline: C
1738
+ name: IGHV3-66_star_02_113
1739
+ transitions:
1740
+ IGHV3-66_star_02_114: 1.0
1741
+ - !!python/object:python.hmmwriter.State
1742
+ emissions:
1743
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1744
+ A: 0.036749014910624996
1745
+ C: 0.889752955268125
1746
+ G: 0.036749014910624996
1747
+ T: 0.036749014910624996
1748
+ track: nukes
1749
+ extras:
1750
+ ambiguous_char: N
1751
+ ambiguous_emission_prob: 0.25
1752
+ germline: C
1753
+ name: IGHV3-66_star_02_114
1754
+ transitions:
1755
+ IGHV3-66_star_02_115: 1.0
1756
+ - !!python/object:python.hmmwriter.State
1757
+ emissions:
1758
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1759
+ A: 0.889752955268125
1760
+ C: 0.036749014910624996
1761
+ G: 0.036749014910624996
1762
+ T: 0.036749014910624996
1763
+ track: nukes
1764
+ extras:
1765
+ ambiguous_char: N
1766
+ ambiguous_emission_prob: 0.25
1767
+ germline: A
1768
+ name: IGHV3-66_star_02_115
1769
+ transitions:
1770
+ IGHV3-66_star_02_116: 1.0
1771
+ - !!python/object:python.hmmwriter.State
1772
+ emissions:
1773
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1774
+ A: 0.036749014910624996
1775
+ C: 0.036749014910624996
1776
+ G: 0.889752955268125
1777
+ T: 0.036749014910624996
1778
+ track: nukes
1779
+ extras:
1780
+ ambiguous_char: N
1781
+ ambiguous_emission_prob: 0.25
1782
+ germline: G
1783
+ name: IGHV3-66_star_02_116
1784
+ transitions:
1785
+ IGHV3-66_star_02_117: 1.0
1786
+ - !!python/object:python.hmmwriter.State
1787
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1788
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1789
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1790
+ C: 0.03833333333333333
1791
+ G: 0.885
1792
+ T: 0.03833333333333333
1793
+ track: nukes
1794
+ extras:
1795
+ ambiguous_char: N
1796
+ ambiguous_emission_prob: 0.25
1797
+ germline: G
1798
+ name: IGHV3-66_star_02_117
1799
+ transitions:
1800
+ IGHV3-66_star_02_118: 1.0
1801
+ - !!python/object:python.hmmwriter.State
1802
+ emissions:
1803
+ probs:
1804
+ A: 0.036749014910624996
1805
+ C: 0.889752955268125
1806
+ G: 0.036749014910624996
1807
+ T: 0.036749014910624996
1808
+ track: nukes
1809
+ extras:
1810
+ ambiguous_char: N
1811
+ ambiguous_emission_prob: 0.25
1812
+ germline: C
1813
+ name: IGHV3-66_star_02_118
1814
+ transitions:
1815
+ IGHV3-66_star_02_119: 1.0
1816
+ - !!python/object:python.hmmwriter.State
1817
+ emissions:
1818
+ probs:
1819
+ A: 0.036749014910624996
1820
+ C: 0.036749014910624996
1821
+ G: 0.036749014910624996
1822
+ T: 0.889752955268125
1823
+ track: nukes
1824
+ extras:
1825
+ ambiguous_char: N
1826
+ ambiguous_emission_prob: 0.25
1827
+ germline: T
1828
+ name: IGHV3-66_star_02_119
1829
+ transitions:
1830
+ IGHV3-66_star_02_120: 1.0
1831
+ - !!python/object:python.hmmwriter.State
1832
+ emissions:
1833
+ probs:
1834
+ A: 0.036749014910624996
1835
+ C: 0.889752955268125
1836
+ G: 0.036749014910624996
1837
+ T: 0.036749014910624996
1838
+ track: nukes
1839
+ extras:
1840
+ ambiguous_char: N
1841
+ ambiguous_emission_prob: 0.25
1842
+ germline: C
1843
+ name: IGHV3-66_star_02_120
1844
+ transitions:
1845
+ IGHV3-66_star_02_121: 1.0
1846
+ - !!python/object:python.hmmwriter.State
1847
+ emissions:
1848
+ probs:
1849
+ A: 0.036749014910624996
1850
+ C: 0.889752955268125
1851
+ G: 0.036749014910624996
1852
+ T: 0.036749014910624996
1853
+ track: nukes
1854
+ extras:
1855
+ ambiguous_char: N
1856
+ ambiguous_emission_prob: 0.25
1857
+ germline: C
1858
+ name: IGHV3-66_star_02_121
1859
+ transitions:
1860
+ IGHV3-66_star_02_122: 1.0
1861
+ - !!python/object:python.hmmwriter.State
1862
+ emissions:
1863
+ probs:
1864
+ A: 0.889752955268125
1865
+ C: 0.036749014910624996
1866
+ G: 0.036749014910624996
1867
+ T: 0.036749014910624996
1868
+ track: nukes
1869
+ extras:
1870
+ ambiguous_char: N
1871
+ ambiguous_emission_prob: 0.25
1872
+ germline: A
1873
+ name: IGHV3-66_star_02_122
1874
+ transitions:
1875
+ IGHV3-66_star_02_123: 1.0
1876
+ - !!python/object:python.hmmwriter.State
1877
+ emissions:
1878
+ probs:
1879
+ A: 0.03125
1880
+ C: 0.125
1881
+ G: 0.8125
1882
+ T: 0.03125
1883
+ track: nukes
1884
+ extras:
1885
+ ambiguous_char: N
1886
+ ambiguous_emission_prob: 0.25
1887
+ germline: G
1888
+ name: IGHV3-66_star_02_123
1889
+ transitions:
1890
+ IGHV3-66_star_02_124: 1.0
1891
+ - !!python/object:python.hmmwriter.State
1892
+ emissions:
1893
+ probs:
1894
+ A: 0.036749014910624996
1895
+ C: 0.036749014910624996
1896
+ G: 0.889752955268125
1897
+ T: 0.036749014910624996
1898
+ track: nukes
1899
+ extras:
1900
+ ambiguous_char: N
1901
+ ambiguous_emission_prob: 0.25
1902
+ germline: G
1903
+ name: IGHV3-66_star_02_124
1904
+ transitions:
1905
+ IGHV3-66_star_02_125: 1.0
1906
+ - !!python/object:python.hmmwriter.State
1907
+ emissions:
1908
+ probs:
1909
+ A: 0.036749014910624996
1910
+ C: 0.036749014910624996
1911
+ G: 0.889752955268125
1912
+ T: 0.036749014910624996
1913
+ track: nukes
1914
+ extras:
1915
+ ambiguous_char: N
1916
+ ambiguous_emission_prob: 0.25
1917
+ germline: G
1918
+ name: IGHV3-66_star_02_125
1919
+ transitions:
1920
+ IGHV3-66_star_02_126: 1.0
1921
+ - !!python/object:python.hmmwriter.State
1922
+ emissions:
1923
+ probs:
1924
+ A: 0.889752955268125
1925
+ C: 0.036749014910624996
1926
+ G: 0.036749014910624996
1927
+ T: 0.036749014910624996
1928
+ track: nukes
1929
+ extras:
1930
+ ambiguous_char: N
1931
+ ambiguous_emission_prob: 0.25
1932
+ germline: A
1933
+ name: IGHV3-66_star_02_126
1934
+ transitions:
1935
+ IGHV3-66_star_02_127: 1.0
1936
+ - !!python/object:python.hmmwriter.State
1937
+ emissions:
1938
+ probs:
1939
+ A: 0.889752955268125
1940
+ C: 0.036749014910624996
1941
+ G: 0.036749014910624996
1942
+ T: 0.036749014910624996
1943
+ track: nukes
1944
+ extras:
1945
+ ambiguous_char: N
1946
+ ambiguous_emission_prob: 0.25
1947
+ germline: A
1948
+ name: IGHV3-66_star_02_127
1949
+ transitions:
1950
+ IGHV3-66_star_02_128: 1.0
1951
+ - !!python/object:python.hmmwriter.State
1952
+ emissions:
1953
+ probs:
1954
+ A: 0.03833333333333333
1955
+ C: 0.03833333333333333
1956
+ G: 0.885
1957
+ T: 0.03833333333333333
1958
+ track: nukes
1959
+ extras:
1960
+ ambiguous_char: N
1961
+ ambiguous_emission_prob: 0.25
1962
+ germline: G
1963
+ name: IGHV3-66_star_02_128
1964
+ transitions:
1965
+ IGHV3-66_star_02_129: 1.0
1966
+ - !!python/object:python.hmmwriter.State
1967
+ emissions:
1968
+ probs:
1969
+ A: 0.03833333333333333
1970
+ C: 0.03833333333333333
1971
+ G: 0.885
1972
+ T: 0.03833333333333333
1973
+ track: nukes
1974
+ extras:
1975
+ ambiguous_char: N
1976
+ ambiguous_emission_prob: 0.25
1977
+ germline: G
1978
+ name: IGHV3-66_star_02_129
1979
+ transitions:
1980
+ IGHV3-66_star_02_130: 1.0
1981
+ - !!python/object:python.hmmwriter.State
1982
+ emissions:
1983
+ probs:
1984
+ A: 0.036749014910624996
1985
+ C: 0.036749014910624996
1986
+ G: 0.889752955268125
1987
+ T: 0.036749014910624996
1988
+ track: nukes
1989
+ extras:
1990
+ ambiguous_char: N
1991
+ ambiguous_emission_prob: 0.25
1992
+ germline: G
1993
+ name: IGHV3-66_star_02_130
1994
+ transitions:
1995
+ IGHV3-66_star_02_131: 1.0
1996
+ - !!python/object:python.hmmwriter.State
1997
+ emissions:
1998
+ probs:
1999
+ A: 0.036749014910624996
2000
+ C: 0.036749014910624996
2001
+ G: 0.889752955268125
2002
+ T: 0.036749014910624996
2003
+ track: nukes
2004
+ extras:
2005
+ ambiguous_char: N
2006
+ ambiguous_emission_prob: 0.25
2007
+ germline: G
2008
+ name: IGHV3-66_star_02_131
2009
+ transitions:
2010
+ IGHV3-66_star_02_132: 1.0
2011
+ - !!python/object:python.hmmwriter.State
2012
+ emissions:
2013
+ probs:
2014
+ A: 0.036749014910624996
2015
+ C: 0.889752955268125
2016
+ G: 0.036749014910624996
2017
+ T: 0.036749014910624996
2018
+ track: nukes
2019
+ extras:
2020
+ ambiguous_char: N
2021
+ ambiguous_emission_prob: 0.25
2022
+ germline: C
2023
+ name: IGHV3-66_star_02_132
2024
+ transitions:
2025
+ IGHV3-66_star_02_133: 1.0
2026
+ - !!python/object:python.hmmwriter.State
2027
+ emissions:
2028
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2029
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2030
+ C: 0.036749014910624996
2031
+ G: 0.036749014910624996
2032
+ T: 0.889752955268125
2033
+ track: nukes
2034
+ extras:
2035
+ ambiguous_char: N
2036
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2037
+ germline: T
2038
+ name: IGHV3-66_star_02_133
2039
+ transitions:
2040
+ IGHV3-66_star_02_134: 1.0
2041
+ - !!python/object:python.hmmwriter.State
2042
+ emissions:
2043
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2044
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2045
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2046
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2047
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2048
+ track: nukes
2049
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2050
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2051
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2052
+ germline: G
2053
+ name: IGHV3-66_star_02_134
2054
+ transitions:
2055
+ IGHV3-66_star_02_135: 1.0
2056
+ - !!python/object:python.hmmwriter.State
2057
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2058
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2059
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2060
+ C: 0.036749014910624996
2061
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2062
+ T: 0.036749014910624996
2063
+ track: nukes
2064
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2065
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2066
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2067
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2068
+ name: IGHV3-66_star_02_135
2069
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2070
+ IGHV3-66_star_02_136: 1.0
2071
+ - !!python/object:python.hmmwriter.State
2072
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2073
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2074
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2075
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2076
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2077
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2078
+ track: nukes
2079
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2080
+ ambiguous_char: N
2081
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2082
+ germline: A
2083
+ name: IGHV3-66_star_02_136
2084
+ transitions:
2085
+ IGHV3-66_star_02_137: 1.0
2086
+ - !!python/object:python.hmmwriter.State
2087
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2088
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2089
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2090
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2091
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2092
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2093
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2094
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2095
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2096
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2097
+ germline: G
2098
+ name: IGHV3-66_star_02_137
2099
+ transitions:
2100
+ IGHV3-66_star_02_138: 1.0
2101
+ - !!python/object:python.hmmwriter.State
2102
+ emissions:
2103
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2104
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2105
+ C: 0.036749014910624996
2106
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2107
+ T: 0.889752955268125
2108
+ track: nukes
2109
+ extras:
2110
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2111
+ ambiguous_emission_prob: 0.25
2112
+ germline: T
2113
+ name: IGHV3-66_star_02_138
2114
+ transitions:
2115
+ IGHV3-66_star_02_139: 1.0
2116
+ - !!python/object:python.hmmwriter.State
2117
+ emissions:
2118
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2119
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2120
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2121
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2122
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2123
+ track: nukes
2124
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2125
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2126
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2127
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2128
+ name: IGHV3-66_star_02_139
2129
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2130
+ IGHV3-66_star_02_140: 1.0
2131
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2132
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2133
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2134
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2135
+ C: 0.03833333333333333
2136
+ G: 0.885
2137
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2138
+ track: nukes
2139
+ extras:
2140
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2141
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2142
+ germline: G
2143
+ name: IGHV3-66_star_02_140
2144
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2145
+ IGHV3-66_star_02_141: 1.0
2146
+ - !!python/object:python.hmmwriter.State
2147
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2148
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2149
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2150
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2151
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2152
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2153
+ track: nukes
2154
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2155
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2156
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2157
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2158
+ name: IGHV3-66_star_02_141
2159
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2160
+ IGHV3-66_star_02_142: 1.0
2161
+ - !!python/object:python.hmmwriter.State
2162
+ emissions:
2163
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2164
+ A: 0.036749014910624996
2165
+ C: 0.036749014910624996
2166
+ G: 0.036749014910624996
2167
+ T: 0.889752955268125
2168
+ track: nukes
2169
+ extras:
2170
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2171
+ ambiguous_emission_prob: 0.25
2172
+ germline: T
2173
+ name: IGHV3-66_star_02_142
2174
+ transitions:
2175
+ IGHV3-66_star_02_143: 1.0
2176
+ - !!python/object:python.hmmwriter.State
2177
+ emissions:
2178
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2179
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2180
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2181
+ G: 0.03833333333333333
2182
+ T: 0.03833333333333333
2183
+ track: nukes
2184
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2185
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2186
+ ambiguous_emission_prob: 0.25
2187
+ germline: C
2188
+ name: IGHV3-66_star_02_143
2189
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2190
+ IGHV3-66_star_02_144: 1.0
2191
+ - !!python/object:python.hmmwriter.State
2192
+ emissions:
2193
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2194
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2195
+ C: 0.036749014910624996
2196
+ G: 0.036749014910624996
2197
+ T: 0.889752955268125
2198
+ track: nukes
2199
+ extras:
2200
+ ambiguous_char: N
2201
+ ambiguous_emission_prob: 0.25
2202
+ germline: T
2203
+ name: IGHV3-66_star_02_144
2204
+ transitions:
2205
+ IGHV3-66_star_02_145: 1.0
2206
+ - !!python/object:python.hmmwriter.State
2207
+ emissions:
2208
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2209
+ A: 0.036749014910624996
2210
+ C: 0.889752955268125
2211
+ G: 0.036749014910624996
2212
+ T: 0.036749014910624996
2213
+ track: nukes
2214
+ extras:
2215
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2216
+ ambiguous_emission_prob: 0.25
2217
+ germline: C
2218
+ name: IGHV3-66_star_02_145
2219
+ transitions:
2220
+ IGHV3-66_star_02_146: 1.0
2221
+ - !!python/object:python.hmmwriter.State
2222
+ emissions:
2223
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2224
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2225
+ C: 0.036749014910624996
2226
+ G: 0.036749014910624996
2227
+ T: 0.036749014910624996
2228
+ track: nukes
2229
+ extras:
2230
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2231
+ ambiguous_emission_prob: 0.25
2232
+ germline: A
2233
+ name: IGHV3-66_star_02_146
2234
+ transitions:
2235
+ IGHV3-66_star_02_147: 1.0
2236
+ - !!python/object:python.hmmwriter.State
2237
+ emissions:
2238
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2239
+ A: 0.036749014910624996
2240
+ C: 0.036749014910624996
2241
+ G: 0.889752955268125
2242
+ T: 0.036749014910624996
2243
+ track: nukes
2244
+ extras:
2245
+ ambiguous_char: N
2246
+ ambiguous_emission_prob: 0.25
2247
+ germline: G
2248
+ name: IGHV3-66_star_02_147
2249
+ transitions:
2250
+ IGHV3-66_star_02_148: 1.0
2251
+ - !!python/object:python.hmmwriter.State
2252
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2253
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2254
+ A: 0.036749014910624996
2255
+ C: 0.036749014910624996
2256
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2257
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2258
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2259
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2261
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2263
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2264
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2265
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2266
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2267
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2270
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2271
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2273
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2274
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2276
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2277
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2278
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2279
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2280
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2281
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2282
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2283
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2284
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2285
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2286
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2287
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2288
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2289
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2290
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2291
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2292
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2293
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2294
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2295
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2296
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2297
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2300
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2301
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2302
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2303
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2306
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2307
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2308
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2309
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2310
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2311
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2312
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2315
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2316
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2317
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2318
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2319
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2320
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2321
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2322
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2323
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2324
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2325
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2326
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2327
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2328
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2329
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2330
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2331
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2332
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2333
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2334
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2335
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2336
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2337
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2338
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2339
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2340
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2341
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2342
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2343
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2344
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2345
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2346
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2347
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2348
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2349
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2351
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2352
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2353
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2354
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2355
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2356
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2357
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2358
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2359
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2360
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2361
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2362
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2363
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2364
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2365
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2366
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2367
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2368
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2369
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2370
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2371
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2372
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2373
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2374
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2375
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2376
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2377
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2378
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2379
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2381
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2382
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2383
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2384
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2385
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2386
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2387
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2389
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2390
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2391
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2392
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2393
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2394
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2396
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2397
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2398
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2399
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2400
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2401
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2402
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2404
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2405
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2406
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2407
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2408
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2409
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2411
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2412
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2413
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2414
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2415
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2416
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2417
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2419
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2420
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2421
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2422
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2423
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2424
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2425
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2426
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2427
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2428
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2429
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2430
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2431
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2432
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2435
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2436
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2437
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2438
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2439
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2441
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2442
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2443
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2444
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2445
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2446
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2447
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2449
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2450
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2451
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2452
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2453
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2454
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2455
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2456
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2457
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2458
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2459
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2460
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2461
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2462
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2463
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2464
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2465
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2466
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2467
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2468
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2469
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2470
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2471
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2472
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2473
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2474
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2475
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2476
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2477
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2478
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2479
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2480
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2481
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2482
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2483
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2484
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2485
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2486
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2487
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2488
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2489
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2490
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2491
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2492
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2493
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2494
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2495
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2496
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2497
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2498
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2499
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2500
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2501
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2502
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2503
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2504
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2505
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2506
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2507
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2508
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2509
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2510
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2511
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2512
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2513
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2514
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2515
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2516
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2517
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2518
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2519
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2520
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2521
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2522
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2523
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2524
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2525
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2526
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2527
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2528
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2529
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2530
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2531
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2532
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2533
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2534
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2535
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2536
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2537
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2538
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2539
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2540
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2541
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2542
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2543
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2544
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2546
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2547
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2548
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2549
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2550
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2551
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2552
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2553
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2554
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2555
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2556
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2557
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2558
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2559
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2560
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2561
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2562
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2563
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2564
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2565
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2566
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2567
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2570
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2571
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2572
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2573
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2574
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2575
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2576
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2577
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2578
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2579
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2580
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2581
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2582
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2583
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2584
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2585
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2586
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2587
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2588
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2589
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2591
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2592
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2593
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2594
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2595
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2596
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2597
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2598
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2599
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2600
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2601
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2602
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2603
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2604
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2605
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2606
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2607
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2608
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2609
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2610
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2611
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2612
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2613
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2615
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2616
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2617
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2618
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2619
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2621
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2622
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2623
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2624
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2625
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2626
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2627
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2629
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2630
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2631
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2632
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2634
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2636
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2637
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2638
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2639
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2641
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2642
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2643
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2645
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2646
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2647
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2649
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2651
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2652
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2653
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2654
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2655
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2656
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2657
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2664
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2666
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2668
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2669
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2671
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2672
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2683
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2684
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2687
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2696
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2698
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2699
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2700
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2701
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2702
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2713
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2716
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2717
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2726
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2728
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2729
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2731
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2732
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2744
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2746
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2747
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2752
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2756
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2758
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2759
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2761
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2762
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2774
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2775
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2777
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2789
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2790
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2792
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2797
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2801
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2804
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2805
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2806
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2807
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2816
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2817
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2818
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2819
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2820
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2821
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2822
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2823
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2824
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2825
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2826
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2827
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2828
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2829
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2830
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2831
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2832
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2833
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2834
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2835
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2836
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2837
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2838
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2839
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2840
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2841
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2842
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2843
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2844
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2845
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2846
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2847
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2848
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2849
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2850
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2851
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2852
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2853
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2854
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2855
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2856
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2857
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2858
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2859
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2860
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2861
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2862
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2863
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2864
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2865
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2866
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2867
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2868
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2869
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2870
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2871
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2872
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2873
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2874
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2875
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2876
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2877
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2878
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2879
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2880
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2881
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2882
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2883
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2884
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2885
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2886
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2887
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2888
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2889
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2890
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2891
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2892
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2893
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2894
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2895
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2896
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2897
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2898
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2899
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2900
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2901
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2902
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2903
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2904
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2905
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2906
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2907
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2908
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2909
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2910
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2911
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2912
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2913
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2914
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2915
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2916
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2917
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2918
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2919
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2920
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2921
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2922
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2923
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2924
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2925
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2926
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2927
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2928
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2929
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2930
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2931
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2932
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2933
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2934
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2935
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2936
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2937
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2938
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2939
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2940
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2941
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2942
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2943
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2944
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2945
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2946
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2947
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2948
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2949
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2950
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2951
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2952
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2953
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2954
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2955
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2956
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2957
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2958
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2959
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2960
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2961
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2962
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2963
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2964
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2965
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2966
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2967
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2968
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2969
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2970
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2971
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2972
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2973
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2974
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2975
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2976
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2977
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2978
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2979
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2980
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2981
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2982
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2983
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2984
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2985
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2986
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2987
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2988
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2989
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2990
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2991
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2992
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2993
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2994
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2995
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2996
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2997
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2998
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2999
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3000
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3001
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3002
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3003
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3004
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3005
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3006
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3007
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3008
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3009
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3010
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3011
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3012
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3013
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3014
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3015
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3016
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3017
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3018
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3019
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3020
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3021
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3022
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3023
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3024
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3025
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3026
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3027
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3028
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3029
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3030
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3031
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3032
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3033
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3034
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3035
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3036
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3037
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3038
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3039
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3040
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3041
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3042
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3043
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3044
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3045
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3046
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3047
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3048
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3049
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3050
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3051
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3052
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3053
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3054
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3055
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3056
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3057
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3058
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3059
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3060
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3061
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3062
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3063
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3064
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3065
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3066
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3067
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3068
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3069
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3070
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3071
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3072
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3073
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3074
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3075
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3076
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3077
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3078
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3079
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3080
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3081
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3082
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3083
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3084
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3085
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3086
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3087
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3088
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3089
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3090
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3091
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3092
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3093
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3094
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3095
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3096
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3097
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3098
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3099
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3100
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3101
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3102
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3103
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3104
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3105
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3106
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3107
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3108
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3109
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3110
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3111
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3112
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3113
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3114
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3115
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3116
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3117
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3118
+ name: IGHV3-66_star_02_205
3119
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3120
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3121
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3122
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3123
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3124
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3125
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3126
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3127
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3128
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3129
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3130
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3131
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3132
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3133
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3134
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3135
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3136
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3137
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3138
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3139
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3140
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3141
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3142
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3143
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3144
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3145
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3146
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3147
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3148
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3149
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3150
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3151
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3152
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3153
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3154
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3155
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3156
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3157
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3158
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3159
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3160
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3161
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3162
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3163
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3164
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3165
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3166
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3167
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3168
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3169
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3170
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3171
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3172
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3173
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3174
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3175
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3176
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3177
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3178
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3179
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3180
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3181
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3182
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3183
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3184
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3185
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3186
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3187
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3188
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3189
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3190
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3191
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3192
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3193
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3194
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3195
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3196
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3197
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3198
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3199
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3200
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3201
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3202
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3203
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3204
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3205
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3206
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3207
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3208
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3209
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3210
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3211
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3212
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3213
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3214
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3215
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3216
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3217
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3218
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3219
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3220
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3221
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3222
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3223
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3224
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3225
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3226
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3227
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3228
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3229
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3230
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3231
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3232
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3233
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3234
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3235
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3236
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3237
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3238
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3239
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3240
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3241
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3242
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3243
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3244
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3245
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3246
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3247
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3248
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3249
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3250
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3251
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3252
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3253
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3254
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3255
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3256
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3257
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3258
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3259
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3260
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3261
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3262
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3263
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3264
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3265
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3266
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3267
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3268
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3269
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3270
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3271
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3272
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3273
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3274
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3275
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3276
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3277
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3278
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3279
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3280
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3281
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3282
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3283
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3284
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3285
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3286
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3287
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3288
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3289
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3290
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3291
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3292
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3293
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3294
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3295
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3296
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3297
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3298
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3299
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3300
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3301
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3302
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3303
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3304
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3305
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3306
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3307
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3308
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3309
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3310
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3311
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3312
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3313
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3314
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3315
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3316
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3317
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3318
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3319
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3320
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3321
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3322
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3323
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3324
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3325
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3326
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3327
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3328
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3329
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3330
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3331
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3332
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3333
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3334
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3335
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3336
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3337
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3338
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3339
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3340
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3341
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3342
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3343
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3344
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3345
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3346
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3347
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3348
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3349
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3350
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3351
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3352
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3353
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3354
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3355
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3356
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3357
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3358
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3359
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3360
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3361
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3362
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3363
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3364
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3365
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3366
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3367
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3368
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3369
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3370
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3371
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3372
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3373
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3374
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3375
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3376
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3377
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3378
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3379
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3380
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3381
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3382
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3383
+ track: nukes
3384
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3385
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3386
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3387
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3388
+ name: IGHV3-66_star_02_223
3389
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3390
+ IGHV3-66_star_02_224: 1.0
3391
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3392
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3393
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3394
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3395
+ C: 0.036749014910624996
3396
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3397
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3398
+ track: nukes
3399
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3400
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3401
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3402
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3403
+ name: IGHV3-66_star_02_224
3404
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3405
+ IGHV3-66_star_02_225: 1.0
3406
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3407
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3408
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3409
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3410
+ C: 0.036749014910624996
3411
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3412
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3413
+ track: nukes
3414
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3415
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3416
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3417
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3418
+ name: IGHV3-66_star_02_225
3419
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3420
+ IGHV3-66_star_02_226: 1.0
3421
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3422
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3423
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3424
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3425
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3426
+ G: 0.03833333333333333
3427
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3428
+ track: nukes
3429
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3430
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3431
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3432
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3433
+ name: IGHV3-66_star_02_226
3434
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3435
+ IGHV3-66_star_02_227: 1.0
3436
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3437
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3438
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3439
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3440
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3441
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3442
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3443
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3444
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3445
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3446
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3447
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3448
+ name: IGHV3-66_star_02_227
3449
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3450
+ IGHV3-66_star_02_228: 1.0
3451
+ - !!python/object:python.hmmwriter.State
3452
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3453
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3454
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3455
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3456
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3457
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3458
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3459
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3460
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3461
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3462
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3463
+ name: IGHV3-66_star_02_228
3464
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3465
+ IGHV3-66_star_02_229: 1.0
3466
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3467
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3468
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3469
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3470
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3471
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3472
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3473
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3474
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3475
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3476
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3477
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3478
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3479
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3480
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3481
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3482
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3483
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3484
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3485
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3486
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3487
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3488
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3489
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3490
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3491
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3492
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3493
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3494
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3495
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3496
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3497
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3498
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3499
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3500
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3501
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3502
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3503
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3504
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3505
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3506
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3507
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3508
+ name: IGHV3-66_star_02_231
3509
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3510
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3511
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3512
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3513
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3514
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3515
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3516
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3517
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3518
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3519
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3520
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3521
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3522
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3523
+ name: IGHV3-66_star_02_232
3524
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3525
+ IGHV3-66_star_02_233: 1.0
3526
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3527
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3528
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3529
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3530
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3531
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3532
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3533
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3534
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3535
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3536
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3537
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3538
+ name: IGHV3-66_star_02_233
3539
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3540
+ IGHV3-66_star_02_234: 1.0
3541
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3542
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3543
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3544
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3545
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3546
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3547
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3548
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3549
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3550
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3551
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3552
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3553
+ name: IGHV3-66_star_02_234
3554
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3555
+ IGHV3-66_star_02_235: 1.0
3556
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3557
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3558
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3559
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3560
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3561
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3562
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3563
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3564
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3565
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3566
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3567
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3568
+ name: IGHV3-66_star_02_235
3569
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3570
+ IGHV3-66_star_02_236: 1.0
3571
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3572
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3573
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3574
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3575
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3576
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3577
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3578
+ track: nukes
3579
+ extras:
3580
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3581
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3582
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3583
+ name: IGHV3-66_star_02_236
3584
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3585
+ IGHV3-66_star_02_237: 1.0
3586
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3587
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3588
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3589
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3590
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3591
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3592
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3593
+ track: nukes
3594
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3595
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3596
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3597
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3598
+ name: IGHV3-66_star_02_237
3599
+ transitions:
3600
+ IGHV3-66_star_02_238: 1.0
3601
+ - !!python/object:python.hmmwriter.State
3602
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3603
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3604
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3605
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3606
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3607
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3608
+ track: nukes
3609
+ extras:
3610
+ ambiguous_char: N
3611
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3612
+ germline: T
3613
+ name: IGHV3-66_star_02_238
3614
+ transitions:
3615
+ IGHV3-66_star_02_239: 1.0
3616
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3617
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3618
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3619
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3620
+ C: 0.036749014910624996
3621
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3622
+ T: 0.889752955268125
3623
+ track: nukes
3624
+ extras:
3625
+ ambiguous_char: N
3626
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3627
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3628
+ name: IGHV3-66_star_02_239
3629
+ transitions:
3630
+ IGHV3-66_star_02_240: 1.0
3631
+ - !!python/object:python.hmmwriter.State
3632
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3633
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3634
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3635
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3636
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3637
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3638
+ track: nukes
3639
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3640
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3641
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3642
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3643
+ name: IGHV3-66_star_02_240
3644
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3645
+ IGHV3-66_star_02_241: 1.0
3646
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3647
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3648
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3649
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3650
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3651
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3652
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3653
+ track: nukes
3654
+ extras:
3655
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3656
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3657
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3658
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3659
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3660
+ IGHV3-66_star_02_242: 1.0
3661
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3662
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3663
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3664
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3665
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3666
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3667
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3668
+ track: nukes
3669
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3670
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3671
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3672
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3673
+ name: IGHV3-66_star_02_242
3674
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3675
+ IGHV3-66_star_02_243: 1.0
3676
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3677
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3678
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3679
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3680
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3681
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3682
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3683
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3684
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3685
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3686
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3687
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3688
+ name: IGHV3-66_star_02_243
3689
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3690
+ IGHV3-66_star_02_244: 1.0
3691
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3692
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3693
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3694
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3695
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3696
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3697
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3698
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3699
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3700
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3701
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3702
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3703
+ name: IGHV3-66_star_02_244
3704
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3705
+ IGHV3-66_star_02_245: 1.0
3706
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3707
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3708
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3709
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3710
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3711
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3712
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3713
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3714
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3715
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3716
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3717
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3718
+ name: IGHV3-66_star_02_245
3719
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3720
+ IGHV3-66_star_02_246: 1.0
3721
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3722
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3723
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3724
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3725
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3726
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3727
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3728
+ track: nukes
3729
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3730
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3731
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3732
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3733
+ name: IGHV3-66_star_02_246
3734
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3735
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3736
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3737
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3738
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3739
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3740
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3741
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3742
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3743
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3744
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3745
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3746
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3747
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3748
+ name: IGHV3-66_star_02_247
3749
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3750
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3751
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3752
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3753
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3754
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3755
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3756
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3757
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3758
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3759
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3760
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3761
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3762
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3763
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3764
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3765
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3766
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3767
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3768
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3769
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3770
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3771
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3772
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3773
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3774
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3775
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3776
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3777
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3778
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3779
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3780
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3781
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3782
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3783
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3784
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3785
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3786
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3787
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3788
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3789
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3790
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3791
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3792
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3793
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3794
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3795
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3796
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3797
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3798
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3799
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3800
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3801
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3802
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3803
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3804
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3805
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3806
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3807
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3808
+ name: IGHV3-66_star_02_251
3809
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3810
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3811
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3812
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3813
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3814
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3815
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3816
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3817
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3818
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3819
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3820
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3821
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3822
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3823
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3824
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3825
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3826
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3827
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3828
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3829
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3830
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3831
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3832
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3833
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3834
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3835
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3836
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3837
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3838
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3839
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3840
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3841
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3842
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3843
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3844
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3845
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3846
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3847
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3848
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3849
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3850
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3851
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3852
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3853
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3854
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3855
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3856
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3857
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3858
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3859
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3860
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3861
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3862
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3863
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3864
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3865
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3866
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3867
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3868
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3869
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3870
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3871
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3872
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3873
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3874
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3875
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3876
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3877
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3878
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3879
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3880
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3881
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3882
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3883
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3884
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3885
+ IGHV3-66_star_02_257: 1.0
3886
+ - !!python/object:python.hmmwriter.State
3887
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3888
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3889
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3890
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3891
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3892
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3893
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3894
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3895
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3896
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3897
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3898
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3899
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3900
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3901
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3902
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3903
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3904
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3905
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3906
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3907
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3908
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3909
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3910
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3911
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3912
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3913
+ name: IGHV3-66_star_02_258
3914
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3915
+ IGHV3-66_star_02_259: 1.0
3916
+ - !!python/object:python.hmmwriter.State
3917
+ emissions:
3918
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3919
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3920
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3921
+ G: 0.03666666666666667
3922
+ T: 0.03666666666666667
3923
+ track: nukes
3924
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3925
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3926
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3927
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3928
+ name: IGHV3-66_star_02_259
3929
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3930
+ IGHV3-66_star_02_260: 1.0
3931
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3932
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3933
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3934
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3935
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