partis-bcr 1.0.11.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (652) hide show
  1. bin/partis +1 -1
  2. bin/partis-test.py +6 -0
  3. bin/partis.py +1 -1
  4. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/RECORD +652 -125
  7. python/recombinator.py +2 -0
  8. python/treegenerator.py +1 -1
  9. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  10. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +8 -0
  11. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  12. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  13. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  14. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  15. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  16. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  17. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  18. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  19. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +8 -0
  20. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  21. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  22. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  23. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  24. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  25. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  26. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  27. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  28. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  29. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +7 -0
  30. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +7 -0
  31. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +5 -0
  32. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +6 -0
  33. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +7 -0
  34. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  35. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  36. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  37. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +7 -0
  38. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  39. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  40. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  41. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  42. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  43. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  44. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  45. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  46. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  47. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  48. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  49. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  50. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  51. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  52. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  53. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  54. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  55. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  56. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  57. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  58. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  59. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  60. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  61. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  62. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  63. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  64. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  65. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  66. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  67. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  68. test/new-results/annotate-new-simu.yaml +1 -0
  69. test/new-results/cache-new-partition.csv +59 -0
  70. test/new-results/get-selection-metrics-new-simu.yaml +1 -0
  71. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  72. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  73. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  74. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  75. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  76. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  77. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  78. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  79. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  80. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  81. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  82. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  83. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  84. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  85. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  86. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  87. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  88. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  89. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  90. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  91. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  92. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  93. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  94. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  95. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  96. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  97. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  98. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  99. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  100. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  101. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  102. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  103. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  104. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  105. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  106. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  107. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  108. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  109. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  110. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  111. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  112. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  113. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  114. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  115. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  116. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  117. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  118. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  119. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  120. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  121. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  122. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  123. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  124. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  125. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  126. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  127. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  128. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  129. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  130. test/new-results/multi-annotate-new-simu.yaml +1 -0
  131. test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
  132. test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
  133. test/new-results/partition-new-simu/fasttree/iclust-0/log +23 -0
  134. test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
  135. test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
  136. test/new-results/partition-new-simu/fasttree/iclust-1/log +23 -0
  137. test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
  138. test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
  139. test/new-results/partition-new-simu/fasttree/iclust-2/log +22 -0
  140. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  141. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  142. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  143. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  144. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  145. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  146. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  147. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  148. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  149. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  150. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  151. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  152. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  153. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  154. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  155. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  156. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  157. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  158. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  159. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  160. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  161. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  162. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  163. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  164. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  165. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  166. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  167. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  168. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  169. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  170. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  171. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  172. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  173. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  174. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  175. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  176. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  177. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  178. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  179. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  180. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  181. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  182. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  183. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  184. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  185. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  186. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  187. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  188. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  189. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  190. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  191. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  192. test/new-results/partition-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  193. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  194. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  195. test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  196. test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  197. test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  198. test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  199. test/new-results/partition-new-simu.yaml +1 -0
  200. test/new-results/run-times.csv +10 -0
  201. test/new-results/seed-partition-new-simu.yaml +1 -0
  202. test/new-results/test/parameters/data/hmm/all-mean-mute-freqs.csv +43 -0
  203. test/new-results/test/parameters/data/hmm/all-mean-n-muted.csv +155 -0
  204. test/new-results/test/parameters/data/hmm/all-probs.csv +44 -0
  205. test/new-results/test/parameters/data/hmm/cluster_size.csv +2 -0
  206. test/new-results/test/parameters/data/hmm/d-mean-mute-freqs.csv +43 -0
  207. test/new-results/test/parameters/data/hmm/d-mean-n-muted.csv +14 -0
  208. test/new-results/test/parameters/data/hmm/d_gene-d_3p_del-probs.csv +34 -0
  209. test/new-results/test/parameters/data/hmm/d_gene-d_5p_del-probs.csv +42 -0
  210. test/new-results/test/parameters/data/hmm/d_gene-probs.csv +20 -0
  211. test/new-results/test/parameters/data/hmm/d_gene-vd_insertion-probs.csv +39 -0
  212. test/new-results/test/parameters/data/hmm/dj_insertion_content.csv +5 -0
  213. test/new-results/test/parameters/data/hmm/fv_insertion-probs.csv +4 -0
  214. test/new-results/test/parameters/data/hmm/germline-sets/igh/extras.csv +23 -0
  215. test/new-results/test/parameters/data/hmm/germline-sets/igh/ighd.fasta +38 -0
  216. test/new-results/test/parameters/data/hmm/germline-sets/igh/ighj.fasta +14 -0
  217. test/new-results/test/parameters/data/hmm/germline-sets/igh/ighv.fasta +30 -0
  218. test/new-results/test/parameters/data/hmm/hmms/IGHD1-20_star_01.yaml +449 -0
  219. test/new-results/test/parameters/data/hmm/hmms/IGHD1-26_star_01.yaml +512 -0
  220. test/new-results/test/parameters/data/hmm/hmms/IGHD2-15_star_01.yaml +743 -0
  221. test/new-results/test/parameters/data/hmm/hmms/IGHD2-21_star_01.yaml +681 -0
  222. test/new-results/test/parameters/data/hmm/hmms/IGHD2-21_star_02.yaml +681 -0
  223. test/new-results/test/parameters/data/hmm/hmms/IGHD2-2_star_01.yaml +743 -0
  224. test/new-results/test/parameters/data/hmm/hmms/IGHD2-8_star_01.yaml +744 -0
  225. test/new-results/test/parameters/data/hmm/hmms/IGHD2-8_star_02.yaml +743 -0
  226. test/new-results/test/parameters/data/hmm/hmms/IGHD3-10_star_01.yaml +743 -0
  227. test/new-results/test/parameters/data/hmm/hmms/IGHD3-10_star_03.yaml +744 -0
  228. test/new-results/test/parameters/data/hmm/hmms/IGHD3-16_star_02.yaml +870 -0
  229. test/new-results/test/parameters/data/hmm/hmms/IGHD3-22_star_01.yaml +743 -0
  230. test/new-results/test/parameters/data/hmm/hmms/IGHD3-3_star_01.yaml +744 -0
  231. test/new-results/test/parameters/data/hmm/hmms/IGHD4-17_star_01.yaml +429 -0
  232. test/new-results/test/parameters/data/hmm/hmms/IGHD4-4_star_01.yaml +428 -0
  233. test/new-results/test/parameters/data/hmm/hmms/IGHD5-5_star_01.yaml +513 -0
  234. test/new-results/test/parameters/data/hmm/hmms/IGHD6-13_star_01.yaml +533 -0
  235. test/new-results/test/parameters/data/hmm/hmms/IGHD6-19_star_01.yaml +534 -0
  236. test/new-results/test/parameters/data/hmm/hmms/IGHD6-6_star_01.yaml +470 -0
  237. test/new-results/test/parameters/data/hmm/hmms/IGHJ1_star_01.yaml +986 -0
  238. test/new-results/test/parameters/data/hmm/hmms/IGHJ2_star_01.yaml +1006 -0
  239. test/new-results/test/parameters/data/hmm/hmms/IGHJ3_star_02.yaml +946 -0
  240. test/new-results/test/parameters/data/hmm/hmms/IGHJ4_star_02.yaml +906 -0
  241. test/new-results/test/parameters/data/hmm/hmms/IGHJ5_star_02.yaml +966 -0
  242. test/new-results/test/parameters/data/hmm/hmms/IGHJ6_star_02.yaml +1206 -0
  243. test/new-results/test/parameters/data/hmm/hmms/IGHJ6_star_03.yaml +1206 -0
  244. test/new-results/test/parameters/data/hmm/hmms/IGHV1-18_star_01.yaml +4484 -0
  245. test/new-results/test/parameters/data/hmm/hmms/IGHV1-2_star_02.yaml +4484 -0
  246. test/new-results/test/parameters/data/hmm/hmms/IGHV2-5_star_02.yaml +4560 -0
  247. test/new-results/test/parameters/data/hmm/hmms/IGHV2-70D_star_04.yaml +4561 -0
  248. test/new-results/test/parameters/data/hmm/hmms/IGHV3-11_star_04.yaml +4484 -0
  249. test/new-results/test/parameters/data/hmm/hmms/IGHV3-23_star_01.yaml +4484 -0
  250. test/new-results/test/parameters/data/hmm/hmms/IGHV3-66_star_02.yaml +4439 -0
  251. test/new-results/test/parameters/data/hmm/hmms/IGHV3-69-1_star_02.yaml +4439 -0
  252. test/new-results/test/parameters/data/hmm/hmms/IGHV3-7_star_05.yaml +4484 -0
  253. test/new-results/test/parameters/data/hmm/hmms/IGHV3-9_star_02.yaml +4516 -0
  254. test/new-results/test/parameters/data/hmm/hmms/IGHV4-34_star_01.yaml +4439 -0
  255. test/new-results/test/parameters/data/hmm/hmms/IGHV4-39_star_09.yaml +4529 -0
  256. test/new-results/test/parameters/data/hmm/hmms/IGHV4-4_star_09.yaml +4438 -0
  257. test/new-results/test/parameters/data/hmm/hmms/IGHV4-61_star_01.yaml +4529 -0
  258. test/new-results/test/parameters/data/hmm/hmms/IGHV5-51_star_01.yaml +4484 -0
  259. test/new-results/test/parameters/data/hmm/j-mean-mute-freqs.csv +43 -0
  260. test/new-results/test/parameters/data/hmm/j-mean-n-muted.csv +25 -0
  261. test/new-results/test/parameters/data/hmm/j_gene-dj_insertion-probs.csv +31 -0
  262. test/new-results/test/parameters/data/hmm/j_gene-j_3p_del-probs.csv +8 -0
  263. test/new-results/test/parameters/data/hmm/j_gene-j_5p_del-probs.csv +31 -0
  264. test/new-results/test/parameters/data/hmm/j_gene-probs.csv +8 -0
  265. test/new-results/test/parameters/data/hmm/jf_insertion-probs.csv +3 -0
  266. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD1-20_star_01.csv +8 -0
  267. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD1-26_star_01.csv +8 -0
  268. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-15_star_01.csv +32 -0
  269. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-21_star_01.csv +17 -0
  270. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-21_star_02.csv +29 -0
  271. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-2_star_01.csv +10 -0
  272. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-8_star_01.csv +32 -0
  273. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-8_star_02.csv +9 -0
  274. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD3-10_star_01.csv +27 -0
  275. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD3-10_star_03.csv +14 -0
  276. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD3-16_star_02.csv +35 -0
  277. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD3-22_star_01.csv +32 -0
  278. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD3-3_star_01.csv +21 -0
  279. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD4-17_star_01.csv +12 -0
  280. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD4-4_star_01.csv +12 -0
  281. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD5-5_star_01.csv +13 -0
  282. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD6-13_star_01.csv +22 -0
  283. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD6-19_star_01.csv +22 -0
  284. test/new-results/test/parameters/data/hmm/mute-freqs/IGHD6-6_star_01.csv +19 -0
  285. test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ1_star_01.csv +52 -0
  286. test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ2_star_01.csv +54 -0
  287. test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ3_star_02.csv +51 -0
  288. test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ4_star_02.csv +49 -0
  289. test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ5_star_02.csv +50 -0
  290. test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ6_star_02.csv +33 -0
  291. test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ6_star_03.csv +40 -0
  292. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV1-18_star_01.csv +297 -0
  293. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV1-2_star_02.csv +296 -0
  294. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV2-5_star_02.csv +66 -0
  295. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV2-70D_star_04.csv +89 -0
  296. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-11_star_04.csv +73 -0
  297. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-23_star_01.csv +297 -0
  298. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-66_star_02.csv +294 -0
  299. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-69-1_star_02.csv +38 -0
  300. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-7_star_05.csv +70 -0
  301. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-9_star_02.csv +40 -0
  302. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV4-34_star_01.csv +40 -0
  303. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV4-39_star_09.csv +40 -0
  304. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV4-4_star_09.csv +59 -0
  305. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV4-61_star_01.csv +300 -0
  306. test/new-results/test/parameters/data/hmm/mute-freqs/IGHV5-51_star_01.csv +296 -0
  307. test/new-results/test/parameters/data/hmm/seq_content.csv +5 -0
  308. test/new-results/test/parameters/data/hmm/v-mean-mute-freqs.csv +43 -0
  309. test/new-results/test/parameters/data/hmm/v-mean-n-muted.csv +122 -0
  310. test/new-results/test/parameters/data/hmm/v_gene-probs.csv +16 -0
  311. test/new-results/test/parameters/data/hmm/v_gene-v_3p_del-probs.csv +24 -0
  312. test/new-results/test/parameters/data/hmm/v_gene-v_5p_del-probs.csv +16 -0
  313. test/new-results/test/parameters/data/hmm/vd_insertion_content.csv +5 -0
  314. test/new-results/test/parameters/data/sw/all-mean-mute-freqs.csv +43 -0
  315. test/new-results/test/parameters/data/sw/all-mean-n-muted.csv +155 -0
  316. test/new-results/test/parameters/data/sw/all-probs.csv +44 -0
  317. test/new-results/test/parameters/data/sw/cluster_size.csv +2 -0
  318. test/new-results/test/parameters/data/sw/d-mean-mute-freqs.csv +43 -0
  319. test/new-results/test/parameters/data/sw/d-mean-n-muted.csv +14 -0
  320. test/new-results/test/parameters/data/sw/d_gene-d_3p_del-probs.csv +40 -0
  321. test/new-results/test/parameters/data/sw/d_gene-d_5p_del-probs.csv +42 -0
  322. test/new-results/test/parameters/data/sw/d_gene-probs.csv +23 -0
  323. test/new-results/test/parameters/data/sw/d_gene-vd_insertion-probs.csv +40 -0
  324. test/new-results/test/parameters/data/sw/dj_insertion_content.csv +5 -0
  325. test/new-results/test/parameters/data/sw/fv_insertion-probs.csv +3 -0
  326. test/new-results/test/parameters/data/sw/germline-sets/igh/extras.csv +26 -0
  327. test/new-results/test/parameters/data/sw/germline-sets/igh/ighd.fasta +44 -0
  328. test/new-results/test/parameters/data/sw/germline-sets/igh/ighj.fasta +14 -0
  329. test/new-results/test/parameters/data/sw/germline-sets/igh/ighv.fasta +36 -0
  330. test/new-results/test/parameters/data/sw/hmms/IGHD1-1_star_01.yaml +450 -0
  331. test/new-results/test/parameters/data/sw/hmms/IGHD1-20_star_01.yaml +449 -0
  332. test/new-results/test/parameters/data/sw/hmms/IGHD1-26_star_01.yaml +512 -0
  333. test/new-results/test/parameters/data/sw/hmms/IGHD2-15_star_01.yaml +744 -0
  334. test/new-results/test/parameters/data/sw/hmms/IGHD2-21_star_01.yaml +681 -0
  335. test/new-results/test/parameters/data/sw/hmms/IGHD2-21_star_02.yaml +681 -0
  336. test/new-results/test/parameters/data/sw/hmms/IGHD2-2_star_01.yaml +743 -0
  337. test/new-results/test/parameters/data/sw/hmms/IGHD2-8_star_01.yaml +744 -0
  338. test/new-results/test/parameters/data/sw/hmms/IGHD2-8_star_02.yaml +743 -0
  339. test/new-results/test/parameters/data/sw/hmms/IGHD3-10_star_01.yaml +743 -0
  340. test/new-results/test/parameters/data/sw/hmms/IGHD3-10_star_03.yaml +744 -0
  341. test/new-results/test/parameters/data/sw/hmms/IGHD3-16_star_02.yaml +869 -0
  342. test/new-results/test/parameters/data/sw/hmms/IGHD3-16_star_03.yaml +869 -0
  343. test/new-results/test/parameters/data/sw/hmms/IGHD3-22_star_01.yaml +743 -0
  344. test/new-results/test/parameters/data/sw/hmms/IGHD3-3_star_01.yaml +744 -0
  345. test/new-results/test/parameters/data/sw/hmms/IGHD4-17_star_01.yaml +429 -0
  346. test/new-results/test/parameters/data/sw/hmms/IGHD4-4_star_01.yaml +428 -0
  347. test/new-results/test/parameters/data/sw/hmms/IGHD5-5_star_01.yaml +513 -0
  348. test/new-results/test/parameters/data/sw/hmms/IGHD6-13_star_01.yaml +533 -0
  349. test/new-results/test/parameters/data/sw/hmms/IGHD6-19_star_01.yaml +533 -0
  350. test/new-results/test/parameters/data/sw/hmms/IGHD6-25_star_01.yaml +470 -0
  351. test/new-results/test/parameters/data/sw/hmms/IGHD6-6_star_01.yaml +470 -0
  352. test/new-results/test/parameters/data/sw/hmms/IGHJ1_star_01.yaml +986 -0
  353. test/new-results/test/parameters/data/sw/hmms/IGHJ2_star_01.yaml +1006 -0
  354. test/new-results/test/parameters/data/sw/hmms/IGHJ3_star_02.yaml +946 -0
  355. test/new-results/test/parameters/data/sw/hmms/IGHJ4_star_02.yaml +906 -0
  356. test/new-results/test/parameters/data/sw/hmms/IGHJ5_star_02.yaml +966 -0
  357. test/new-results/test/parameters/data/sw/hmms/IGHJ6_star_02.yaml +1206 -0
  358. test/new-results/test/parameters/data/sw/hmms/IGHJ6_star_03.yaml +1206 -0
  359. test/new-results/test/parameters/data/sw/hmms/IGHV1-18_star_01.yaml +4484 -0
  360. test/new-results/test/parameters/data/sw/hmms/IGHV1-2_star_02.yaml +4484 -0
  361. test/new-results/test/parameters/data/sw/hmms/IGHV2-5_star_02.yaml +4560 -0
  362. test/new-results/test/parameters/data/sw/hmms/IGHV2-70D_star_04.yaml +4561 -0
  363. test/new-results/test/parameters/data/sw/hmms/IGHV3-11_star_04.yaml +4484 -0
  364. test/new-results/test/parameters/data/sw/hmms/IGHV3-23_star_01.yaml +4484 -0
  365. test/new-results/test/parameters/data/sw/hmms/IGHV3-23_star_03.yaml +4484 -0
  366. test/new-results/test/parameters/data/sw/hmms/IGHV3-30_star_04.yaml +4484 -0
  367. test/new-results/test/parameters/data/sw/hmms/IGHV3-48_star_03.yaml +4484 -0
  368. test/new-results/test/parameters/data/sw/hmms/IGHV3-66_star_02.yaml +4439 -0
  369. test/new-results/test/parameters/data/sw/hmms/IGHV3-69-1_star_02.yaml +4439 -0
  370. test/new-results/test/parameters/data/sw/hmms/IGHV3-7_star_05.yaml +4484 -0
  371. test/new-results/test/parameters/data/sw/hmms/IGHV3-9_star_02.yaml +4516 -0
  372. test/new-results/test/parameters/data/sw/hmms/IGHV4-34_star_01.yaml +4439 -0
  373. test/new-results/test/parameters/data/sw/hmms/IGHV4-39_star_09.yaml +4529 -0
  374. test/new-results/test/parameters/data/sw/hmms/IGHV4-4_star_09.yaml +4438 -0
  375. test/new-results/test/parameters/data/sw/hmms/IGHV4-61_star_01.yaml +4529 -0
  376. test/new-results/test/parameters/data/sw/hmms/IGHV5-51_star_01.yaml +4484 -0
  377. test/new-results/test/parameters/data/sw/j-mean-mute-freqs.csv +43 -0
  378. test/new-results/test/parameters/data/sw/j-mean-n-muted.csv +25 -0
  379. test/new-results/test/parameters/data/sw/j_gene-dj_insertion-probs.csv +32 -0
  380. test/new-results/test/parameters/data/sw/j_gene-j_3p_del-probs.csv +11 -0
  381. test/new-results/test/parameters/data/sw/j_gene-j_5p_del-probs.csv +31 -0
  382. test/new-results/test/parameters/data/sw/j_gene-probs.csv +8 -0
  383. test/new-results/test/parameters/data/sw/jf_insertion-probs.csv +3 -0
  384. test/new-results/test/parameters/data/sw/mute-freqs/IGHD1-1_star_01.csv +4 -0
  385. test/new-results/test/parameters/data/sw/mute-freqs/IGHD1-20_star_01.csv +8 -0
  386. test/new-results/test/parameters/data/sw/mute-freqs/IGHD1-26_star_01.csv +8 -0
  387. test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-15_star_01.csv +32 -0
  388. test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-21_star_01.csv +28 -0
  389. test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-21_star_02.csv +27 -0
  390. test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-2_star_01.csv +27 -0
  391. test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-8_star_01.csv +32 -0
  392. test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-8_star_02.csv +12 -0
  393. test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-10_star_01.csv +29 -0
  394. test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-10_star_03.csv +14 -0
  395. test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-16_star_02.csv +34 -0
  396. test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-16_star_03.csv +20 -0
  397. test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-22_star_01.csv +30 -0
  398. test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-3_star_01.csv +21 -0
  399. test/new-results/test/parameters/data/sw/mute-freqs/IGHD4-17_star_01.csv +12 -0
  400. test/new-results/test/parameters/data/sw/mute-freqs/IGHD4-4_star_01.csv +9 -0
  401. test/new-results/test/parameters/data/sw/mute-freqs/IGHD5-5_star_01.csv +9 -0
  402. test/new-results/test/parameters/data/sw/mute-freqs/IGHD6-13_star_01.csv +20 -0
  403. test/new-results/test/parameters/data/sw/mute-freqs/IGHD6-19_star_01.csv +21 -0
  404. test/new-results/test/parameters/data/sw/mute-freqs/IGHD6-25_star_01.csv +12 -0
  405. test/new-results/test/parameters/data/sw/mute-freqs/IGHD6-6_star_01.csv +19 -0
  406. test/new-results/test/parameters/data/sw/mute-freqs/IGHJ1_star_01.csv +52 -0
  407. test/new-results/test/parameters/data/sw/mute-freqs/IGHJ2_star_01.csv +54 -0
  408. test/new-results/test/parameters/data/sw/mute-freqs/IGHJ3_star_02.csv +51 -0
  409. test/new-results/test/parameters/data/sw/mute-freqs/IGHJ4_star_02.csv +49 -0
  410. test/new-results/test/parameters/data/sw/mute-freqs/IGHJ5_star_02.csv +51 -0
  411. test/new-results/test/parameters/data/sw/mute-freqs/IGHJ6_star_02.csv +33 -0
  412. test/new-results/test/parameters/data/sw/mute-freqs/IGHJ6_star_03.csv +40 -0
  413. test/new-results/test/parameters/data/sw/mute-freqs/IGHV1-18_star_01.csv +297 -0
  414. test/new-results/test/parameters/data/sw/mute-freqs/IGHV1-2_star_02.csv +296 -0
  415. test/new-results/test/parameters/data/sw/mute-freqs/IGHV2-5_star_02.csv +66 -0
  416. test/new-results/test/parameters/data/sw/mute-freqs/IGHV2-70D_star_04.csv +89 -0
  417. test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-11_star_04.csv +73 -0
  418. test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-23_star_01.csv +297 -0
  419. test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-23_star_03.csv +32 -0
  420. test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-30_star_04.csv +38 -0
  421. test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-48_star_03.csv +38 -0
  422. test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-66_star_02.csv +292 -0
  423. test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-69-1_star_02.csv +38 -0
  424. test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-7_star_05.csv +70 -0
  425. test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-9_star_02.csv +40 -0
  426. test/new-results/test/parameters/data/sw/mute-freqs/IGHV4-34_star_01.csv +40 -0
  427. test/new-results/test/parameters/data/sw/mute-freqs/IGHV4-39_star_09.csv +40 -0
  428. test/new-results/test/parameters/data/sw/mute-freqs/IGHV4-4_star_09.csv +59 -0
  429. test/new-results/test/parameters/data/sw/mute-freqs/IGHV4-61_star_01.csv +300 -0
  430. test/new-results/test/parameters/data/sw/mute-freqs/IGHV5-51_star_01.csv +296 -0
  431. test/new-results/test/parameters/data/sw/seq_content.csv +5 -0
  432. test/new-results/test/parameters/data/sw/v-mean-mute-freqs.csv +43 -0
  433. test/new-results/test/parameters/data/sw/v-mean-n-muted.csv +122 -0
  434. test/new-results/test/parameters/data/sw/v_gene-probs.csv +19 -0
  435. test/new-results/test/parameters/data/sw/v_gene-v_3p_del-probs.csv +25 -0
  436. test/new-results/test/parameters/data/sw/v_gene-v_5p_del-probs.csv +29 -0
  437. test/new-results/test/parameters/data/sw/vd_insertion_content.csv +5 -0
  438. test/new-results/test/parameters/data/sw-cache.yaml +1 -0
  439. test/new-results/test/parameters/simu/hmm/all-mean-mute-freqs.csv +3 -3
  440. test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv +11 -11
  441. test/new-results/test/parameters/simu/hmm/all-probs.csv +13 -3
  442. test/new-results/test/parameters/simu/hmm/cluster_size.csv +1 -1
  443. test/new-results/test/parameters/simu/hmm/d-mean-mute-freqs.csv +6 -6
  444. test/new-results/test/parameters/simu/hmm/d-mean-n-muted.csv +3 -3
  445. test/new-results/test/parameters/simu/hmm/d_gene-d_3p_del-probs.csv +6 -1
  446. test/new-results/test/parameters/simu/hmm/d_gene-d_5p_del-probs.csv +9 -2
  447. test/new-results/test/parameters/simu/hmm/d_gene-probs.csv +5 -1
  448. test/new-results/test/parameters/simu/hmm/d_gene-vd_insertion-probs.csv +10 -2
  449. test/new-results/test/parameters/simu/hmm/dj_insertion_content.csv +4 -4
  450. test/new-results/test/parameters/simu/hmm/fv_insertion-probs.csv +3 -2
  451. test/new-results/test/parameters/simu/hmm/germline-sets/igh/extras.csv +6 -0
  452. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighd.fasta +8 -0
  453. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighj.fasta +2 -0
  454. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighv.fasta +10 -0
  455. test/new-results/test/parameters/simu/hmm/hmms/IGHD1-20_star_01.yaml +449 -0
  456. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-16_star_02.yaml +870 -0
  457. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-22_star_01.yaml +744 -0
  458. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-13_star_01.yaml +267 -268
  459. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-19_star_01.yaml +534 -0
  460. test/new-results/test/parameters/simu/hmm/hmms/IGHJ1_star_01.yaml +986 -0
  461. test/new-results/test/parameters/simu/hmm/hmms/IGHJ4_star_02.yaml +306 -306
  462. test/new-results/test/parameters/simu/hmm/hmms/IGHJ6_star_02.yaml +284 -284
  463. test/new-results/test/parameters/simu/hmm/hmms/IGHV1-18_star_01.yaml +4484 -0
  464. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-23_star_01.yaml +4484 -0
  465. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-66_star_02.yaml +1191 -1191
  466. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-7_star_05.yaml +2 -2
  467. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-4_star_09.yaml +4438 -0
  468. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-61_star_01.yaml +4529 -0
  469. test/new-results/test/parameters/simu/hmm/hmms/IGHV5-51_star_01.yaml +4484 -0
  470. test/new-results/test/parameters/simu/hmm/j-mean-mute-freqs.csv +5 -5
  471. test/new-results/test/parameters/simu/hmm/j-mean-n-muted.csv +4 -4
  472. test/new-results/test/parameters/simu/hmm/j_gene-dj_insertion-probs.csv +9 -2
  473. test/new-results/test/parameters/simu/hmm/j_gene-j_3p_del-probs.csv +2 -1
  474. test/new-results/test/parameters/simu/hmm/j_gene-j_5p_del-probs.csv +7 -2
  475. test/new-results/test/parameters/simu/hmm/j_gene-probs.csv +2 -1
  476. test/new-results/test/parameters/simu/hmm/jf_insertion-probs.csv +1 -1
  477. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD1-20_star_01.csv +9 -0
  478. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-16_star_02.csv +30 -0
  479. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-22_star_01.csv +32 -0
  480. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-13_star_01.csv +16 -13
  481. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-19_star_01.csv +22 -0
  482. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ1_star_01.csv +50 -0
  483. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ4_star_02.csv +44 -40
  484. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ6_star_02.csv +2 -0
  485. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV1-18_star_01.csv +297 -0
  486. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-23_star_01.csv +297 -0
  487. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-66_star_02.csv +293 -291
  488. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-4_star_09.csv +291 -0
  489. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-61_star_01.csv +300 -0
  490. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV5-51_star_01.csv +296 -0
  491. test/new-results/test/parameters/simu/hmm/seq_content.csv +4 -4
  492. test/new-results/test/parameters/simu/hmm/v-mean-mute-freqs.csv +3 -3
  493. test/new-results/test/parameters/simu/hmm/v-mean-n-muted.csv +7 -7
  494. test/new-results/test/parameters/simu/hmm/v_gene-probs.csv +6 -1
  495. test/new-results/test/parameters/simu/hmm/v_gene-v_3p_del-probs.csv +7 -1
  496. test/new-results/test/parameters/simu/hmm/v_gene-v_5p_del-probs.csv +6 -1
  497. test/new-results/test/parameters/simu/hmm/vd_insertion_content.csv +4 -4
  498. test/new-results/test/parameters/simu/sw/all-mean-mute-freqs.csv +3 -3
  499. test/new-results/test/parameters/simu/sw/all-mean-n-muted.csv +8 -8
  500. test/new-results/test/parameters/simu/sw/all-probs.csv +9 -1
  501. test/new-results/test/parameters/simu/sw/cluster_size.csv +1 -1
  502. test/new-results/test/parameters/simu/sw/d-mean-mute-freqs.csv +5 -5
  503. test/new-results/test/parameters/simu/sw/d-mean-n-muted.csv +3 -3
  504. test/new-results/test/parameters/simu/sw/d_gene-d_3p_del-probs.csv +7 -1
  505. test/new-results/test/parameters/simu/sw/d_gene-d_5p_del-probs.csv +7 -1
  506. test/new-results/test/parameters/simu/sw/d_gene-probs.csv +5 -1
  507. test/new-results/test/parameters/simu/sw/d_gene-vd_insertion-probs.csv +8 -1
  508. test/new-results/test/parameters/simu/sw/dj_insertion_content.csv +4 -4
  509. test/new-results/test/parameters/simu/sw/fv_insertion-probs.csv +1 -1
  510. test/new-results/test/parameters/simu/sw/germline-sets/igh/extras.csv +6 -0
  511. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighd.fasta +8 -0
  512. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighj.fasta +2 -0
  513. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighv.fasta +10 -0
  514. test/new-results/test/parameters/simu/sw/hmms/IGHD1-20_star_01.yaml +449 -0
  515. test/new-results/test/parameters/simu/sw/hmms/IGHD3-16_star_02.yaml +870 -0
  516. test/new-results/test/parameters/simu/sw/hmms/IGHD3-22_star_01.yaml +744 -0
  517. test/new-results/test/parameters/simu/sw/hmms/IGHD6-13_star_01.yaml +267 -268
  518. test/new-results/test/parameters/simu/sw/hmms/IGHD6-19_star_01.yaml +534 -0
  519. test/new-results/test/parameters/simu/sw/hmms/IGHJ1_star_01.yaml +986 -0
  520. test/new-results/test/parameters/simu/sw/hmms/IGHJ4_star_02.yaml +306 -306
  521. test/new-results/test/parameters/simu/sw/hmms/IGHJ6_star_02.yaml +22 -22
  522. test/new-results/test/parameters/simu/sw/hmms/IGHV1-18_star_01.yaml +4484 -0
  523. test/new-results/test/parameters/simu/sw/hmms/IGHV3-23_star_01.yaml +4484 -0
  524. test/new-results/test/parameters/simu/sw/hmms/IGHV3-66_star_02.yaml +1191 -1191
  525. test/new-results/test/parameters/simu/sw/hmms/IGHV3-7_star_05.yaml +2 -2
  526. test/new-results/test/parameters/simu/sw/hmms/IGHV4-4_star_09.yaml +4438 -0
  527. test/new-results/test/parameters/simu/sw/hmms/IGHV4-61_star_01.yaml +4529 -0
  528. test/new-results/test/parameters/simu/sw/hmms/IGHV5-51_star_01.yaml +4484 -0
  529. test/new-results/test/parameters/simu/sw/j-mean-mute-freqs.csv +4 -4
  530. test/new-results/test/parameters/simu/sw/j-mean-n-muted.csv +3 -3
  531. test/new-results/test/parameters/simu/sw/j_gene-dj_insertion-probs.csv +7 -1
  532. test/new-results/test/parameters/simu/sw/j_gene-j_3p_del-probs.csv +2 -1
  533. test/new-results/test/parameters/simu/sw/j_gene-j_5p_del-probs.csv +7 -1
  534. test/new-results/test/parameters/simu/sw/j_gene-probs.csv +2 -1
  535. test/new-results/test/parameters/simu/sw/jf_insertion-probs.csv +1 -1
  536. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD1-20_star_01.csv +9 -0
  537. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-16_star_02.csv +30 -0
  538. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-22_star_01.csv +32 -0
  539. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-13_star_01.csv +16 -13
  540. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-19_star_01.csv +20 -0
  541. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ1_star_01.csv +50 -0
  542. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ4_star_02.csv +48 -40
  543. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV1-18_star_01.csv +297 -0
  544. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-23_star_01.csv +297 -0
  545. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv +293 -291
  546. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-4_star_09.csv +291 -0
  547. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-61_star_01.csv +300 -0
  548. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV5-51_star_01.csv +296 -0
  549. test/new-results/test/parameters/simu/sw/seq_content.csv +4 -4
  550. test/new-results/test/parameters/simu/sw/v-mean-mute-freqs.csv +3 -3
  551. test/new-results/test/parameters/simu/sw/v-mean-n-muted.csv +7 -7
  552. test/new-results/test/parameters/simu/sw/v_gene-probs.csv +6 -1
  553. test/new-results/test/parameters/simu/sw/v_gene-v_3p_del-probs.csv +7 -1
  554. test/new-results/test/parameters/simu/sw/v_gene-v_5p_del-probs.csv +6 -1
  555. test/new-results/test/parameters/simu/sw/vd_insertion_content.csv +4 -4
  556. test/new-results/test/parameters/simu/sw-cache.yaml +1 -1
  557. test/new-results/test/parameters/simu/true/all-mean-mute-freqs.csv +43 -0
  558. test/new-results/test/parameters/simu/true/all-mean-n-muted.csv +155 -0
  559. test/new-results/test/parameters/simu/true/all-probs.csv +10 -0
  560. test/new-results/test/parameters/simu/true/cluster_size.csv +7 -0
  561. test/new-results/test/parameters/simu/true/d-mean-mute-freqs.csv +43 -0
  562. test/new-results/test/parameters/simu/true/d-mean-n-muted.csv +14 -0
  563. test/new-results/test/parameters/simu/true/d_gene-d_3p_del-probs.csv +9 -0
  564. test/new-results/test/parameters/simu/true/d_gene-d_5p_del-probs.csv +10 -0
  565. test/new-results/test/parameters/simu/true/d_gene-probs.csv +7 -0
  566. test/new-results/test/parameters/simu/true/d_gene-vd_insertion-probs.csv +10 -0
  567. test/new-results/test/parameters/simu/true/dj_insertion_content.csv +5 -0
  568. test/new-results/test/parameters/simu/true/fv_insertion-probs.csv +2 -0
  569. test/new-results/test/parameters/simu/true/germline-sets/igh/extras.csv +11 -0
  570. test/new-results/test/parameters/simu/true/germline-sets/igh/ighd.fasta +12 -0
  571. test/new-results/test/parameters/simu/true/germline-sets/igh/ighj.fasta +6 -0
  572. test/new-results/test/parameters/simu/true/germline-sets/igh/ighv.fasta +14 -0
  573. test/new-results/test/parameters/simu/true/j-mean-mute-freqs.csv +43 -0
  574. test/new-results/test/parameters/simu/true/j-mean-n-muted.csv +25 -0
  575. test/new-results/test/parameters/simu/true/j_gene-dj_insertion-probs.csv +7 -0
  576. test/new-results/test/parameters/simu/true/j_gene-j_3p_del-probs.csv +4 -0
  577. test/new-results/test/parameters/simu/true/j_gene-j_5p_del-probs.csv +9 -0
  578. test/new-results/test/parameters/simu/true/j_gene-probs.csv +4 -0
  579. test/new-results/test/parameters/simu/true/jf_insertion-probs.csv +2 -0
  580. test/new-results/test/parameters/simu/true/mute-freqs/IGHD1-20_star_01.csv +8 -0
  581. test/new-results/test/parameters/simu/true/mute-freqs/IGHD3-16_star_02.csv +30 -0
  582. test/new-results/test/parameters/simu/true/mute-freqs/IGHD3-22_star_01.csv +32 -0
  583. test/new-results/test/parameters/simu/true/mute-freqs/IGHD6-13_star_01.csv +22 -0
  584. test/new-results/test/parameters/simu/true/mute-freqs/IGHD6-19_star_01.csv +22 -0
  585. test/new-results/test/parameters/simu/true/mute-freqs/IGHD6-6_star_01.csv +13 -0
  586. test/new-results/test/parameters/simu/true/mute-freqs/IGHJ1_star_01.csv +50 -0
  587. test/new-results/test/parameters/simu/true/mute-freqs/IGHJ4_star_02.csv +45 -0
  588. test/new-results/test/parameters/simu/true/mute-freqs/IGHJ6_star_02.csv +47 -0
  589. test/new-results/test/parameters/simu/true/mute-freqs/IGHV1-18_star_01.csv +297 -0
  590. test/new-results/test/parameters/simu/true/mute-freqs/IGHV3-23_star_01.csv +297 -0
  591. test/new-results/test/parameters/simu/true/mute-freqs/IGHV3-66_star_02.csv +294 -0
  592. test/new-results/test/parameters/simu/true/mute-freqs/IGHV3-7_star_05.csv +297 -0
  593. test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-4_star_09.csv +291 -0
  594. test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-61_star_01.csv +300 -0
  595. test/new-results/test/parameters/simu/true/mute-freqs/IGHV5-51_star_01.csv +296 -0
  596. test/new-results/test/parameters/simu/true/seq_content.csv +5 -0
  597. test/new-results/test/parameters/simu/true/v-mean-mute-freqs.csv +43 -0
  598. test/new-results/test/parameters/simu/true/v-mean-n-muted.csv +122 -0
  599. test/new-results/test/parameters/simu/true/v_gene-probs.csv +8 -0
  600. test/new-results/test/parameters/simu/true/v_gene-v_3p_del-probs.csv +9 -0
  601. test/new-results/test/parameters/simu/true/v_gene-v_5p_del-probs.csv +8 -0
  602. test/new-results/test/parameters/simu/true/vd_insertion_content.csv +5 -0
  603. test/new-results/test/simu.yaml +1 -0
  604. test/new-results/test.log +273 -24
  605. test/new-results/vsearch-partition-new-simu.yaml +1 -0
  606. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  607. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +4 -4
  608. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  609. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  610. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  611. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  612. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  613. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  614. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  615. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  616. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  617. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  618. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  619. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  620. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  621. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  622. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  623. test/paired/new-results/run-times.csv +6 -5
  624. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +2 -2
  625. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +6 -6
  626. test/paired/new-results/subset-partition-new-simu/merged-partition.log +4 -4
  627. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  628. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  629. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  630. test/paired/new-results/test/simu/all-seqs.fa +226 -0
  631. test/paired/new-results/test/simu/igh+igk/igh.yaml +1 -0
  632. test/paired/new-results/test/simu/igh+igk/igk.yaml +1 -0
  633. test/paired/new-results/test/simu/igh+igl/igh.yaml +1 -0
  634. test/paired/new-results/test/simu/igh+igl/igl.yaml +1 -0
  635. test/paired/new-results/test/simu/igh.yaml +1 -0
  636. test/paired/new-results/test/simu/igk.yaml +1 -0
  637. test/paired/new-results/test/simu/igl.yaml +1 -0
  638. test/paired/new-results/test/simu/meta.yaml +1 -0
  639. test/paired/new-results/test.log +227 -33
  640. test/test.py +6 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/gctree-run.py +0 -0
  646. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  647. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/parse-output.py +0 -0
  648. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/split-loci.py +0 -0
  649. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/WHEEL +0 -0
  650. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/entry_points.txt +0 -0
  651. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/licenses/COPYING +0 -0
  652. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/data/sw/hmms/IGHJ5_star_02.yaml ADDED
@@ -0,0 +1,966 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.17391304347826086
4
+ overall_mute_freq: 0.08956521739130437
5
+ per_gene_mute_freq: 0.11894633162227648
6
+ name: IGHJ5_star_02
7
+ states:
8
+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
11
+ name: init
12
+ transitions:
13
+ IGHJ5_star_02_0: 0.0021746517159361195
14
+ IGHJ5_star_02_1: 0.0021746517159361195
15
+ IGHJ5_star_02_10: 0.00326197757390418
16
+ IGHJ5_star_02_11: 0.0021746517159361195
17
+ IGHJ5_star_02_12: 0.0021746517159361195
18
+ IGHJ5_star_02_13: 0.0021746517159361195
19
+ IGHJ5_star_02_14: 0.0021746517159361195
20
+ IGHJ5_star_02_15: 0.0021746517159361195
21
+ IGHJ5_star_02_16: 0.0021746517159361195
22
+ IGHJ5_star_02_17: 0.0020387359836901123
23
+ IGHJ5_star_02_2: 0.0021746517159361195
24
+ IGHJ5_star_02_3: 0.0021746517159361195
25
+ IGHJ5_star_02_4: 0.0021746517159361195
26
+ IGHJ5_star_02_5: 0.0021746517159361195
27
+ IGHJ5_star_02_6: 0.0021746517159361195
28
+ IGHJ5_star_02_7: 0.002899535621248159
29
+ IGHJ5_star_02_8: 0.0036244195265601998
30
+ IGHJ5_star_02_9: 0.004349303431872239
31
+ insert_left_A: 0.20772946859903382
32
+ insert_left_C: 0.2942834138486312
33
+ insert_left_G: 0.2146537842190016
34
+ insert_left_T: 0.2388888888888889
35
+ - !!python/object:python.hmmwriter.State
36
+ emissions:
37
+ probs:
38
+ A: 0.8810536683777235
39
+ C: 0.0396487772074255
40
+ G: 0.0396487772074255
41
+ T: 0.0396487772074255
42
+ track: nukes
43
+ extras:
44
+ ambiguous_char: N
45
+ ambiguous_emission_prob: 0.25
46
+ germline: A
47
+ name: insert_left_A
48
+ transitions:
49
+ IGHJ5_star_02_0: 0.0025415562089865216
50
+ IGHJ5_star_02_1: 0.0025415562089865216
51
+ IGHJ5_star_02_10: 0.003812334313479782
52
+ IGHJ5_star_02_11: 0.0025415562089865216
53
+ IGHJ5_star_02_12: 0.0025415562089865216
54
+ IGHJ5_star_02_13: 0.0025415562089865216
55
+ IGHJ5_star_02_14: 0.0025415562089865216
56
+ IGHJ5_star_02_15: 0.0025415562089865216
57
+ IGHJ5_star_02_16: 0.0025415562089865216
58
+ IGHJ5_star_02_17: 0.002382708945924864
59
+ IGHJ5_star_02_2: 0.0025415562089865216
60
+ IGHJ5_star_02_3: 0.0025415562089865216
61
+ IGHJ5_star_02_4: 0.0025415562089865216
62
+ IGHJ5_star_02_5: 0.0025415562089865216
63
+ IGHJ5_star_02_6: 0.0025415562089865216
64
+ IGHJ5_star_02_7: 0.0033887416119820282
65
+ IGHJ5_star_02_8: 0.004235927014977536
66
+ IGHJ5_star_02_9: 0.005083112417973043
67
+ insert_left_A: 0.20609933586496476
68
+ insert_left_C: 0.2919740591420334
69
+ insert_left_G: 0.21296931372713027
70
+ insert_left_T: 0.2370142362447095
71
+ - !!python/object:python.hmmwriter.State
72
+ emissions:
73
+ probs:
74
+ A: 0.0396487772074255
75
+ C: 0.8810536683777235
76
+ G: 0.0396487772074255
77
+ T: 0.0396487772074255
78
+ track: nukes
79
+ extras:
80
+ ambiguous_char: N
81
+ ambiguous_emission_prob: 0.25
82
+ germline: C
83
+ name: insert_left_C
84
+ transitions:
85
+ IGHJ5_star_02_0: 0.0025415562089865216
86
+ IGHJ5_star_02_1: 0.0025415562089865216
87
+ IGHJ5_star_02_10: 0.003812334313479782
88
+ IGHJ5_star_02_11: 0.0025415562089865216
89
+ IGHJ5_star_02_12: 0.0025415562089865216
90
+ IGHJ5_star_02_13: 0.0025415562089865216
91
+ IGHJ5_star_02_14: 0.0025415562089865216
92
+ IGHJ5_star_02_15: 0.0025415562089865216
93
+ IGHJ5_star_02_16: 0.0025415562089865216
94
+ IGHJ5_star_02_17: 0.002382708945924864
95
+ IGHJ5_star_02_2: 0.0025415562089865216
96
+ IGHJ5_star_02_3: 0.0025415562089865216
97
+ IGHJ5_star_02_4: 0.0025415562089865216
98
+ IGHJ5_star_02_5: 0.0025415562089865216
99
+ IGHJ5_star_02_6: 0.0025415562089865216
100
+ IGHJ5_star_02_7: 0.0033887416119820282
101
+ IGHJ5_star_02_8: 0.004235927014977536
102
+ IGHJ5_star_02_9: 0.005083112417973043
103
+ insert_left_A: 0.20609933586496476
104
+ insert_left_C: 0.2919740591420334
105
+ insert_left_G: 0.21296931372713027
106
+ insert_left_T: 0.2370142362447095
107
+ - !!python/object:python.hmmwriter.State
108
+ emissions:
109
+ probs:
110
+ A: 0.0396487772074255
111
+ C: 0.0396487772074255
112
+ G: 0.8810536683777235
113
+ T: 0.0396487772074255
114
+ track: nukes
115
+ extras:
116
+ ambiguous_char: N
117
+ ambiguous_emission_prob: 0.25
118
+ germline: G
119
+ name: insert_left_G
120
+ transitions:
121
+ IGHJ5_star_02_0: 0.0025415562089865216
122
+ IGHJ5_star_02_1: 0.0025415562089865216
123
+ IGHJ5_star_02_10: 0.003812334313479782
124
+ IGHJ5_star_02_11: 0.0025415562089865216
125
+ IGHJ5_star_02_12: 0.0025415562089865216
126
+ IGHJ5_star_02_13: 0.0025415562089865216
127
+ IGHJ5_star_02_14: 0.0025415562089865216
128
+ IGHJ5_star_02_15: 0.0025415562089865216
129
+ IGHJ5_star_02_16: 0.0025415562089865216
130
+ IGHJ5_star_02_17: 0.002382708945924864
131
+ IGHJ5_star_02_2: 0.0025415562089865216
132
+ IGHJ5_star_02_3: 0.0025415562089865216
133
+ IGHJ5_star_02_4: 0.0025415562089865216
134
+ IGHJ5_star_02_5: 0.0025415562089865216
135
+ IGHJ5_star_02_6: 0.0025415562089865216
136
+ IGHJ5_star_02_7: 0.0033887416119820282
137
+ IGHJ5_star_02_8: 0.004235927014977536
138
+ IGHJ5_star_02_9: 0.005083112417973043
139
+ insert_left_A: 0.20609933586496476
140
+ insert_left_C: 0.2919740591420334
141
+ insert_left_G: 0.21296931372713027
142
+ insert_left_T: 0.2370142362447095
143
+ - !!python/object:python.hmmwriter.State
144
+ emissions:
145
+ probs:
146
+ A: 0.0396487772074255
147
+ C: 0.0396487772074255
148
+ G: 0.0396487772074255
149
+ T: 0.8810536683777235
150
+ track: nukes
151
+ extras:
152
+ ambiguous_char: N
153
+ ambiguous_emission_prob: 0.25
154
+ germline: T
155
+ name: insert_left_T
156
+ transitions:
157
+ IGHJ5_star_02_0: 0.0025415562089865216
158
+ IGHJ5_star_02_1: 0.0025415562089865216
159
+ IGHJ5_star_02_10: 0.003812334313479782
160
+ IGHJ5_star_02_11: 0.0025415562089865216
161
+ IGHJ5_star_02_12: 0.0025415562089865216
162
+ IGHJ5_star_02_13: 0.0025415562089865216
163
+ IGHJ5_star_02_14: 0.0025415562089865216
164
+ IGHJ5_star_02_15: 0.0025415562089865216
165
+ IGHJ5_star_02_16: 0.0025415562089865216
166
+ IGHJ5_star_02_17: 0.002382708945924864
167
+ IGHJ5_star_02_2: 0.0025415562089865216
168
+ IGHJ5_star_02_3: 0.0025415562089865216
169
+ IGHJ5_star_02_4: 0.0025415562089865216
170
+ IGHJ5_star_02_5: 0.0025415562089865216
171
+ IGHJ5_star_02_6: 0.0025415562089865216
172
+ IGHJ5_star_02_7: 0.0033887416119820282
173
+ IGHJ5_star_02_8: 0.004235927014977536
174
+ IGHJ5_star_02_9: 0.005083112417973043
175
+ insert_left_A: 0.20609933586496476
176
+ insert_left_C: 0.2919740591420334
177
+ insert_left_G: 0.21296931372713027
178
+ insert_left_T: 0.2370142362447095
179
+ - !!python/object:python.hmmwriter.State
180
+ emissions:
181
+ probs:
182
+ A: 0.8810536683777235
183
+ C: 0.03964877720742549
184
+ G: 0.03964877720742549
185
+ T: 0.03964877720742549
186
+ track: nukes
187
+ extras:
188
+ ambiguous_char: N
189
+ ambiguous_emission_prob: 0.25
190
+ germline: A
191
+ name: IGHJ5_star_02_0
192
+ transitions:
193
+ IGHJ5_star_02_1: 1.0
194
+ - !!python/object:python.hmmwriter.State
195
+ emissions:
196
+ probs:
197
+ A: 0.0394599311131838
198
+ C: 0.8816202066604486
199
+ G: 0.0394599311131838
200
+ T: 0.0394599311131838
201
+ track: nukes
202
+ extras:
203
+ ambiguous_char: N
204
+ ambiguous_emission_prob: 0.25
205
+ germline: C
206
+ name: IGHJ5_star_02_1
207
+ transitions:
208
+ IGHJ5_star_02_2: 1.0
209
+ - !!python/object:python.hmmwriter.State
210
+ emissions:
211
+ probs:
212
+ A: 0.8815397916873962
213
+ C: 0.03948673610420127
214
+ G: 0.03948673610420127
215
+ T: 0.03948673610420127
216
+ track: nukes
217
+ extras:
218
+ ambiguous_char: N
219
+ ambiguous_emission_prob: 0.25
220
+ germline: A
221
+ name: IGHJ5_star_02_2
222
+ transitions:
223
+ IGHJ5_star_02_3: 1.0
224
+ - !!python/object:python.hmmwriter.State
225
+ emissions:
226
+ probs:
227
+ A: 0.878645618121065
228
+ C: 0.04045146062631167
229
+ G: 0.04045146062631167
230
+ T: 0.04045146062631167
231
+ track: nukes
232
+ extras:
233
+ ambiguous_char: N
234
+ ambiguous_emission_prob: 0.25
235
+ germline: A
236
+ name: IGHJ5_star_02_3
237
+ transitions:
238
+ IGHJ5_star_02_4: 1.0
239
+ - !!python/object:python.hmmwriter.State
240
+ emissions:
241
+ probs:
242
+ A: 0.03948767894222706
243
+ C: 0.8815369631733189
244
+ G: 0.03948767894222706
245
+ T: 0.03948767894222706
246
+ track: nukes
247
+ extras:
248
+ ambiguous_char: N
249
+ ambiguous_emission_prob: 0.25
250
+ germline: C
251
+ name: IGHJ5_star_02_4
252
+ transitions:
253
+ IGHJ5_star_02_5: 1.0
254
+ - !!python/object:python.hmmwriter.State
255
+ emissions:
256
+ probs:
257
+ A: 0.04098658290556912
258
+ C: 0.04098658290556912
259
+ G: 0.04098658290556912
260
+ T: 0.8770402512832927
261
+ track: nukes
262
+ extras:
263
+ ambiguous_char: N
264
+ ambiguous_emission_prob: 0.25
265
+ germline: T
266
+ name: IGHJ5_star_02_5
267
+ transitions:
268
+ IGHJ5_star_02_6: 1.0
269
+ - !!python/object:python.hmmwriter.State
270
+ emissions:
271
+ probs:
272
+ A: 0.03941659697063784
273
+ C: 0.03941659697063784
274
+ G: 0.8817502090880864
275
+ T: 0.03941659697063784
276
+ track: nukes
277
+ extras:
278
+ ambiguous_char: N
279
+ ambiguous_emission_prob: 0.25
280
+ germline: G
281
+ name: IGHJ5_star_02_6
282
+ transitions:
283
+ IGHJ5_star_02_7: 1.0
284
+ - !!python/object:python.hmmwriter.State
285
+ emissions:
286
+ probs:
287
+ A: 0.03937790026450658
288
+ C: 0.03937790026450658
289
+ G: 0.8818662992064803
290
+ T: 0.03937790026450658
291
+ track: nukes
292
+ extras:
293
+ ambiguous_char: N
294
+ ambiguous_emission_prob: 0.25
295
+ germline: G
296
+ name: IGHJ5_star_02_7
297
+ transitions:
298
+ IGHJ5_star_02_8: 1.0
299
+ - !!python/object:python.hmmwriter.State
300
+ emissions:
301
+ probs:
302
+ A: 0.039339203558375294
303
+ C: 0.039339203558375294
304
+ G: 0.039339203558375294
305
+ T: 0.8819823893248742
306
+ track: nukes
307
+ extras:
308
+ ambiguous_char: N
309
+ ambiguous_emission_prob: 0.25
310
+ germline: T
311
+ name: IGHJ5_star_02_8
312
+ transitions:
313
+ IGHJ5_star_02_9: 1.0
314
+ - !!python/object:python.hmmwriter.State
315
+ emissions:
316
+ probs:
317
+ A: 0.039806827464084024
318
+ C: 0.039806827464084024
319
+ G: 0.039806827464084024
320
+ T: 0.8805795176077479
321
+ track: nukes
322
+ extras:
323
+ ambiguous_char: N
324
+ ambiguous_emission_prob: 0.25
325
+ germline: T
326
+ name: IGHJ5_star_02_9
327
+ transitions:
328
+ IGHJ5_star_02_10: 1.0
329
+ - !!python/object:python.hmmwriter.State
330
+ emissions:
331
+ probs:
332
+ A: 0.03982438860371275
333
+ C: 0.8805268341888618
334
+ G: 0.03982438860371275
335
+ T: 0.03982438860371275
336
+ track: nukes
337
+ extras:
338
+ ambiguous_char: N
339
+ ambiguous_emission_prob: 0.25
340
+ germline: C
341
+ name: IGHJ5_star_02_10
342
+ transitions:
343
+ IGHJ5_star_02_11: 1.0
344
+ - !!python/object:python.hmmwriter.State
345
+ emissions:
346
+ probs:
347
+ A: 0.04809194974334147
348
+ C: 0.04809194974334147
349
+ G: 0.8557241507699755
350
+ T: 0.04809194974334147
351
+ track: nukes
352
+ extras:
353
+ ambiguous_char: N
354
+ ambiguous_emission_prob: 0.25
355
+ germline: G
356
+ name: IGHJ5_star_02_11
357
+ transitions:
358
+ IGHJ5_star_02_12: 1.0
359
+ - !!python/object:python.hmmwriter.State
360
+ emissions:
361
+ probs:
362
+ A: 0.8399214673510894
363
+ C: 0.053359510882970196
364
+ G: 0.053359510882970196
365
+ T: 0.053359510882970196
366
+ track: nukes
367
+ extras:
368
+ ambiguous_char: N
369
+ ambiguous_emission_prob: 0.25
370
+ germline: A
371
+ name: IGHJ5_star_02_12
372
+ transitions:
373
+ IGHJ5_star_02_13: 1.0
374
+ - !!python/object:python.hmmwriter.State
375
+ emissions:
376
+ probs:
377
+ A: 0.037763931714505164
378
+ C: 0.8867082048564845
379
+ G: 0.037763931714505164
380
+ T: 0.037763931714505164
381
+ track: nukes
382
+ extras:
383
+ ambiguous_char: N
384
+ ambiguous_emission_prob: 0.25
385
+ germline: C
386
+ name: IGHJ5_star_02_13
387
+ transitions:
388
+ IGHJ5_star_02_14: 1.0
389
+ - !!python/object:python.hmmwriter.State
390
+ emissions:
391
+ probs:
392
+ A: 0.03779597487167073
393
+ C: 0.848816100513317
394
+ G: 0.03779597487167073
395
+ T: 0.07559194974334146
396
+ track: nukes
397
+ extras:
398
+ ambiguous_char: N
399
+ ambiguous_emission_prob: 0.25
400
+ germline: C
401
+ name: IGHJ5_star_02_14
402
+ transitions:
403
+ IGHJ5_star_02_15: 1.0
404
+ - !!python/object:python.hmmwriter.State
405
+ emissions:
406
+ probs:
407
+ A: 0.08518079145278457
408
+ C: 0.8296384170944309
409
+ G: 0.04259039572639228
410
+ T: 0.04259039572639228
411
+ track: nukes
412
+ extras:
413
+ ambiguous_char: N
414
+ ambiguous_emission_prob: 0.25
415
+ germline: C
416
+ name: IGHJ5_star_02_15
417
+ transitions:
418
+ IGHJ5_star_02_16: 1.0
419
+ - !!python/object:python.hmmwriter.State
420
+ emissions:
421
+ probs:
422
+ A: 0.03726308877481844
423
+ C: 0.8882107336755447
424
+ G: 0.03726308877481844
425
+ T: 0.03726308877481844
426
+ track: nukes
427
+ extras:
428
+ ambiguous_char: N
429
+ ambiguous_emission_prob: 0.25
430
+ germline: C
431
+ name: IGHJ5_star_02_16
432
+ transitions:
433
+ IGHJ5_star_02_17: 1.0
434
+ - !!python/object:python.hmmwriter.State
435
+ emissions:
436
+ probs:
437
+ A: 0.03625903638219383
438
+ C: 0.03625903638219383
439
+ G: 0.03625903638219383
440
+ T: 0.8912228908534185
441
+ track: nukes
442
+ extras:
443
+ ambiguous_char: N
444
+ ambiguous_emission_prob: 0.25
445
+ germline: T
446
+ name: IGHJ5_star_02_17
447
+ transitions:
448
+ IGHJ5_star_02_18: 1.0
449
+ - !!python/object:python.hmmwriter.State
450
+ emissions:
451
+ probs:
452
+ A: 0.03605963986306255
453
+ C: 0.03605963986306255
454
+ G: 0.8918210804108123
455
+ T: 0.03605963986306255
456
+ track: nukes
457
+ extras:
458
+ ambiguous_char: N
459
+ ambiguous_emission_prob: 0.25
460
+ germline: G
461
+ name: IGHJ5_star_02_18
462
+ transitions:
463
+ IGHJ5_star_02_19: 1.0
464
+ - !!python/object:python.hmmwriter.State
465
+ emissions:
466
+ probs:
467
+ A: 0.03586024334393127
468
+ C: 0.03586024334393127
469
+ G: 0.8924192699682062
470
+ T: 0.03586024334393127
471
+ track: nukes
472
+ extras:
473
+ ambiguous_char: N
474
+ ambiguous_emission_prob: 0.25
475
+ germline: G
476
+ name: IGHJ5_star_02_19
477
+ transitions:
478
+ IGHJ5_star_02_20: 1.0
479
+ - !!python/object:python.hmmwriter.State
480
+ emissions:
481
+ probs:
482
+ A: 0.0356608468248
483
+ C: 0.0356608468248
484
+ G: 0.8930174595256
485
+ T: 0.0356608468248
486
+ track: nukes
487
+ extras:
488
+ ambiguous_char: N
489
+ ambiguous_emission_prob: 0.25
490
+ germline: G
491
+ name: IGHJ5_star_02_20
492
+ transitions:
493
+ IGHJ5_star_02_21: 1.0
494
+ - !!python/object:python.hmmwriter.State
495
+ emissions:
496
+ probs:
497
+ A: 0.0356608468248
498
+ C: 0.0356608468248
499
+ G: 0.8930174595256
500
+ T: 0.0356608468248
501
+ track: nukes
502
+ extras:
503
+ ambiguous_char: N
504
+ ambiguous_emission_prob: 0.25
505
+ germline: G
506
+ name: IGHJ5_star_02_21
507
+ transitions:
508
+ IGHJ5_star_02_22: 1.0
509
+ - !!python/object:python.hmmwriter.State
510
+ emissions:
511
+ probs:
512
+ A: 0.0356608468248
513
+ C: 0.8930174595256
514
+ G: 0.0356608468248
515
+ T: 0.0356608468248
516
+ track: nukes
517
+ extras:
518
+ ambiguous_char: N
519
+ ambiguous_emission_prob: 0.25
520
+ germline: C
521
+ name: IGHJ5_star_02_22
522
+ transitions:
523
+ IGHJ5_star_02_23: 1.0
524
+ - !!python/object:python.hmmwriter.State
525
+ emissions:
526
+ probs:
527
+ A: 0.0356608468248
528
+ C: 0.8930174595256
529
+ G: 0.0356608468248
530
+ T: 0.0356608468248
531
+ track: nukes
532
+ extras:
533
+ ambiguous_char: N
534
+ ambiguous_emission_prob: 0.25
535
+ germline: C
536
+ name: IGHJ5_star_02_23
537
+ transitions:
538
+ IGHJ5_star_02_24: 1.0
539
+ - !!python/object:python.hmmwriter.State
540
+ emissions:
541
+ probs:
542
+ A: 0.8930174595256
543
+ C: 0.0356608468248
544
+ G: 0.0356608468248
545
+ T: 0.0356608468248
546
+ track: nukes
547
+ extras:
548
+ ambiguous_char: N
549
+ ambiguous_emission_prob: 0.25
550
+ germline: A
551
+ name: IGHJ5_star_02_24
552
+ transitions:
553
+ IGHJ5_star_02_25: 1.0
554
+ - !!python/object:python.hmmwriter.State
555
+ emissions:
556
+ probs:
557
+ A: 0.0356608468248
558
+ C: 0.0356608468248
559
+ G: 0.8930174595256
560
+ T: 0.0356608468248
561
+ track: nukes
562
+ extras:
563
+ ambiguous_char: N
564
+ ambiguous_emission_prob: 0.25
565
+ germline: G
566
+ name: IGHJ5_star_02_25
567
+ transitions:
568
+ IGHJ5_star_02_26: 1.0
569
+ - !!python/object:python.hmmwriter.State
570
+ emissions:
571
+ probs:
572
+ A: 0.0356608468248
573
+ C: 0.0356608468248
574
+ G: 0.8930174595256
575
+ T: 0.0356608468248
576
+ track: nukes
577
+ extras:
578
+ ambiguous_char: N
579
+ ambiguous_emission_prob: 0.25
580
+ germline: G
581
+ name: IGHJ5_star_02_26
582
+ transitions:
583
+ IGHJ5_star_02_27: 1.0
584
+ - !!python/object:python.hmmwriter.State
585
+ emissions:
586
+ probs:
587
+ A: 0.0356608468248
588
+ C: 0.0356608468248
589
+ G: 0.8930174595256
590
+ T: 0.0356608468248
591
+ track: nukes
592
+ extras:
593
+ ambiguous_char: N
594
+ ambiguous_emission_prob: 0.25
595
+ germline: G
596
+ name: IGHJ5_star_02_27
597
+ transitions:
598
+ IGHJ5_star_02_28: 1.0
599
+ - !!python/object:python.hmmwriter.State
600
+ emissions:
601
+ probs:
602
+ A: 0.89
603
+ C: 0.03666666666666667
604
+ G: 0.03666666666666667
605
+ T: 0.03666666666666667
606
+ track: nukes
607
+ extras:
608
+ ambiguous_char: N
609
+ ambiguous_emission_prob: 0.25
610
+ germline: A
611
+ name: IGHJ5_star_02_28
612
+ transitions:
613
+ IGHJ5_star_02_29: 1.0
614
+ - !!python/object:python.hmmwriter.State
615
+ emissions:
616
+ probs:
617
+ A: 0.875
618
+ C: 0.041666666666666664
619
+ G: 0.041666666666666664
620
+ T: 0.041666666666666664
621
+ track: nukes
622
+ extras:
623
+ ambiguous_char: N
624
+ ambiguous_emission_prob: 0.25
625
+ germline: A
626
+ name: IGHJ5_star_02_29
627
+ transitions:
628
+ IGHJ5_star_02_30: 1.0
629
+ - !!python/object:python.hmmwriter.State
630
+ emissions:
631
+ probs:
632
+ A: 0.038435063548083334
633
+ C: 0.88469480935575
634
+ G: 0.038435063548083334
635
+ T: 0.038435063548083334
636
+ track: nukes
637
+ extras:
638
+ ambiguous_char: N
639
+ ambiguous_emission_prob: 0.25
640
+ germline: C
641
+ name: IGHJ5_star_02_30
642
+ transitions:
643
+ IGHJ5_star_02_31: 1.0
644
+ - !!python/object:python.hmmwriter.State
645
+ emissions:
646
+ probs:
647
+ A: 0.038435063548083334
648
+ C: 0.88469480935575
649
+ G: 0.038435063548083334
650
+ T: 0.038435063548083334
651
+ track: nukes
652
+ extras:
653
+ ambiguous_char: N
654
+ ambiguous_emission_prob: 0.25
655
+ germline: C
656
+ name: IGHJ5_star_02_31
657
+ transitions:
658
+ IGHJ5_star_02_32: 1.0
659
+ - !!python/object:python.hmmwriter.State
660
+ emissions:
661
+ probs:
662
+ A: 0.038435063548083334
663
+ C: 0.88469480935575
664
+ G: 0.038435063548083334
665
+ T: 0.038435063548083334
666
+ track: nukes
667
+ extras:
668
+ ambiguous_char: N
669
+ ambiguous_emission_prob: 0.25
670
+ germline: C
671
+ name: IGHJ5_star_02_32
672
+ transitions:
673
+ IGHJ5_star_02_33: 1.0
674
+ - !!python/object:python.hmmwriter.State
675
+ emissions:
676
+ probs:
677
+ A: 0.038435063548083334
678
+ C: 0.038435063548083334
679
+ G: 0.038435063548083334
680
+ T: 0.88469480935575
681
+ track: nukes
682
+ extras:
683
+ ambiguous_char: N
684
+ ambiguous_emission_prob: 0.25
685
+ germline: T
686
+ name: IGHJ5_star_02_33
687
+ transitions:
688
+ IGHJ5_star_02_34: 1.0
689
+ - !!python/object:python.hmmwriter.State
690
+ emissions:
691
+ probs:
692
+ A: 0.038435063548083334
693
+ C: 0.038435063548083334
694
+ G: 0.88469480935575
695
+ T: 0.038435063548083334
696
+ track: nukes
697
+ extras:
698
+ ambiguous_char: N
699
+ ambiguous_emission_prob: 0.25
700
+ germline: G
701
+ name: IGHJ5_star_02_34
702
+ transitions:
703
+ IGHJ5_star_02_35: 1.0
704
+ - !!python/object:python.hmmwriter.State
705
+ emissions:
706
+ probs:
707
+ A: 0.038435063548083334
708
+ C: 0.038435063548083334
709
+ G: 0.88469480935575
710
+ T: 0.038435063548083334
711
+ track: nukes
712
+ extras:
713
+ ambiguous_char: N
714
+ ambiguous_emission_prob: 0.25
715
+ germline: G
716
+ name: IGHJ5_star_02_35
717
+ transitions:
718
+ IGHJ5_star_02_36: 1.0
719
+ - !!python/object:python.hmmwriter.State
720
+ emissions:
721
+ probs:
722
+ A: 0.038435063548083334
723
+ C: 0.038435063548083334
724
+ G: 0.038435063548083334
725
+ T: 0.88469480935575
726
+ track: nukes
727
+ extras:
728
+ ambiguous_char: N
729
+ ambiguous_emission_prob: 0.25
730
+ germline: T
731
+ name: IGHJ5_star_02_36
732
+ transitions:
733
+ IGHJ5_star_02_37: 1.0
734
+ - !!python/object:python.hmmwriter.State
735
+ emissions:
736
+ probs:
737
+ A: 0.038435063548083334
738
+ C: 0.88469480935575
739
+ G: 0.038435063548083334
740
+ T: 0.038435063548083334
741
+ track: nukes
742
+ extras:
743
+ ambiguous_char: N
744
+ ambiguous_emission_prob: 0.25
745
+ germline: C
746
+ name: IGHJ5_star_02_37
747
+ transitions:
748
+ IGHJ5_star_02_38: 1.0
749
+ - !!python/object:python.hmmwriter.State
750
+ emissions:
751
+ probs:
752
+ A: 0.88469480935575
753
+ C: 0.038435063548083334
754
+ G: 0.038435063548083334
755
+ T: 0.038435063548083334
756
+ track: nukes
757
+ extras:
758
+ ambiguous_char: N
759
+ ambiguous_emission_prob: 0.25
760
+ germline: A
761
+ name: IGHJ5_star_02_38
762
+ transitions:
763
+ IGHJ5_star_02_39: 1.0
764
+ - !!python/object:python.hmmwriter.State
765
+ emissions:
766
+ probs:
767
+ A: 0.038435063548083334
768
+ C: 0.88469480935575
769
+ G: 0.038435063548083334
770
+ T: 0.038435063548083334
771
+ track: nukes
772
+ extras:
773
+ ambiguous_char: N
774
+ ambiguous_emission_prob: 0.25
775
+ germline: C
776
+ name: IGHJ5_star_02_39
777
+ transitions:
778
+ IGHJ5_star_02_40: 1.0
779
+ - !!python/object:python.hmmwriter.State
780
+ emissions:
781
+ probs:
782
+ A: 0.038435063548083334
783
+ C: 0.88469480935575
784
+ G: 0.038435063548083334
785
+ T: 0.038435063548083334
786
+ track: nukes
787
+ extras:
788
+ ambiguous_char: N
789
+ ambiguous_emission_prob: 0.25
790
+ germline: C
791
+ name: IGHJ5_star_02_40
792
+ transitions:
793
+ IGHJ5_star_02_41: 1.0
794
+ - !!python/object:python.hmmwriter.State
795
+ emissions:
796
+ probs:
797
+ A: 0.038435063548083334
798
+ C: 0.038435063548083334
799
+ G: 0.88469480935575
800
+ T: 0.038435063548083334
801
+ track: nukes
802
+ extras:
803
+ ambiguous_char: N
804
+ ambiguous_emission_prob: 0.25
805
+ germline: G
806
+ name: IGHJ5_star_02_41
807
+ transitions:
808
+ IGHJ5_star_02_42: 1.0
809
+ - !!python/object:python.hmmwriter.State
810
+ emissions:
811
+ probs:
812
+ A: 0.038435063548083334
813
+ C: 0.038435063548083334
814
+ G: 0.038435063548083334
815
+ T: 0.88469480935575
816
+ track: nukes
817
+ extras:
818
+ ambiguous_char: N
819
+ ambiguous_emission_prob: 0.25
820
+ germline: T
821
+ name: IGHJ5_star_02_42
822
+ transitions:
823
+ IGHJ5_star_02_43: 1.0
824
+ - !!python/object:python.hmmwriter.State
825
+ emissions:
826
+ probs:
827
+ A: 0.038435063548083334
828
+ C: 0.88469480935575
829
+ G: 0.038435063548083334
830
+ T: 0.038435063548083334
831
+ track: nukes
832
+ extras:
833
+ ambiguous_char: N
834
+ ambiguous_emission_prob: 0.25
835
+ germline: C
836
+ name: IGHJ5_star_02_43
837
+ transitions:
838
+ IGHJ5_star_02_44: 1.0
839
+ - !!python/object:python.hmmwriter.State
840
+ emissions:
841
+ probs:
842
+ A: 0.038435063548083334
843
+ C: 0.038435063548083334
844
+ G: 0.038435063548083334
845
+ T: 0.88469480935575
846
+ track: nukes
847
+ extras:
848
+ ambiguous_char: N
849
+ ambiguous_emission_prob: 0.25
850
+ germline: T
851
+ name: IGHJ5_star_02_44
852
+ transitions:
853
+ IGHJ5_star_02_45: 1.0
854
+ - !!python/object:python.hmmwriter.State
855
+ emissions:
856
+ probs:
857
+ A: 0.038435063548083334
858
+ C: 0.88469480935575
859
+ G: 0.038435063548083334
860
+ T: 0.038435063548083334
861
+ track: nukes
862
+ extras:
863
+ ambiguous_char: N
864
+ ambiguous_emission_prob: 0.25
865
+ germline: C
866
+ name: IGHJ5_star_02_45
867
+ transitions:
868
+ IGHJ5_star_02_46: 1.0
869
+ - !!python/object:python.hmmwriter.State
870
+ emissions:
871
+ probs:
872
+ A: 0.038435063548083334
873
+ C: 0.88469480935575
874
+ G: 0.038435063548083334
875
+ T: 0.038435063548083334
876
+ track: nukes
877
+ extras:
878
+ ambiguous_char: N
879
+ ambiguous_emission_prob: 0.25
880
+ germline: C
881
+ name: IGHJ5_star_02_46
882
+ transitions:
883
+ IGHJ5_star_02_47: 1.0
884
+ - !!python/object:python.hmmwriter.State
885
+ emissions:
886
+ probs:
887
+ A: 0.038435063548083334
888
+ C: 0.038435063548083334
889
+ G: 0.038435063548083334
890
+ T: 0.88469480935575
891
+ track: nukes
892
+ extras:
893
+ ambiguous_char: N
894
+ ambiguous_emission_prob: 0.25
895
+ germline: T
896
+ name: IGHJ5_star_02_47
897
+ transitions:
898
+ IGHJ5_star_02_48: 1.0
899
+ - !!python/object:python.hmmwriter.State
900
+ emissions:
901
+ probs:
902
+ A: 0.038435063548083334
903
+ C: 0.88469480935575
904
+ G: 0.038435063548083334
905
+ T: 0.038435063548083334
906
+ track: nukes
907
+ extras:
908
+ ambiguous_char: N
909
+ ambiguous_emission_prob: 0.25
910
+ germline: C
911
+ name: IGHJ5_star_02_48
912
+ transitions:
913
+ IGHJ5_star_02_49: 1.0
914
+ - !!python/object:python.hmmwriter.State
915
+ emissions:
916
+ probs:
917
+ A: 0.875
918
+ C: 0.041666666666666664
919
+ G: 0.041666666666666664
920
+ T: 0.041666666666666664
921
+ track: nukes
922
+ extras:
923
+ ambiguous_char: N
924
+ ambiguous_emission_prob: 0.25
925
+ germline: A
926
+ name: IGHJ5_star_02_49
927
+ transitions:
928
+ IGHJ5_star_02_50: 1.0
929
+ - !!python/object:python.hmmwriter.State
930
+ emissions:
931
+ probs:
932
+ A: 0.038435063548083334
933
+ C: 0.038435063548083334
934
+ G: 0.88469480935575
935
+ T: 0.038435063548083334
936
+ track: nukes
937
+ extras:
938
+ ambiguous_char: N
939
+ ambiguous_emission_prob: 0.25
940
+ germline: G
941
+ name: IGHJ5_star_02_50
942
+ transitions:
943
+ end: 0.04
944
+ insert_right_N: 0.96
945
+ - !!python/object:python.hmmwriter.State
946
+ emissions:
947
+ probs:
948
+ A: 0.25
949
+ C: 0.25
950
+ G: 0.25
951
+ T: 0.25
952
+ track: nukes
953
+ extras:
954
+ ambiguous_char: N
955
+ ambiguous_emission_prob: 0.25
956
+ germline: N
957
+ name: insert_right_N
958
+ transitions:
959
+ end: 0.040000000000000036
960
+ insert_right_N: 0.96
961
+ tracks:
962
+ nukes:
963
+ - A
964
+ - C
965
+ - G
966
+ - T