partis-bcr 1.0.11__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 (655) 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.dev3.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/RECORD +655 -128
  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-0/log +3 -3
  607. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +5 -5
  608. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  609. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +1 -1
  610. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +1 -1
  611. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  612. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  613. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  614. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  615. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  616. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  617. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  618. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  619. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  620. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  621. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  622. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  623. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  624. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  625. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  626. test/paired/new-results/run-times.csv +5 -4
  627. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +5 -9
  628. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +4 -8
  629. test/paired/new-results/subset-partition-new-simu/merged-partition.log +4 -8
  630. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  631. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  632. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  633. test/paired/new-results/test/simu/all-seqs.fa +226 -0
  634. test/paired/new-results/test/simu/igh+igk/igh.yaml +1 -0
  635. test/paired/new-results/test/simu/igh+igk/igk.yaml +1 -0
  636. test/paired/new-results/test/simu/igh+igl/igh.yaml +1 -0
  637. test/paired/new-results/test/simu/igh+igl/igl.yaml +1 -0
  638. test/paired/new-results/test/simu/igh.yaml +1 -0
  639. test/paired/new-results/test/simu/igk.yaml +1 -0
  640. test/paired/new-results/test/simu/igl.yaml +1 -0
  641. test/paired/new-results/test/simu/meta.yaml +1 -0
  642. test/paired/new-results/test.log +225 -40
  643. test/test.py +6 -0
  644. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  645. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  646. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  647. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  648. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/gctree-run.py +0 -0
  649. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  650. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/parse-output.py +0 -0
  651. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/split-loci.py +0 -0
  652. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/WHEEL +0 -0
  653. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/entry_points.txt +0 -0
  654. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/licenses/COPYING +0 -0
  655. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/data/sw/hmms/IGHJ1_star_01.yaml ADDED
@@ -0,0 +1,986 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.08695652173913043
4
+ overall_mute_freq: 0.08956521739130437
5
+ per_gene_mute_freq: 0.12418583179311829
6
+ name: IGHJ1_star_01
7
+ states:
8
+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
11
+ name: init
12
+ transitions:
13
+ IGHJ1_star_01_0: 0.005698005698005698
14
+ IGHJ1_star_01_1: 0.011396011396011397
15
+ IGHJ1_star_01_10: 0.011396011396011397
16
+ IGHJ1_star_01_11: 0.011396011396011397
17
+ IGHJ1_star_01_12: 0.010360010360010361
18
+ IGHJ1_star_01_13: 0.009324009324009324
19
+ IGHJ1_star_01_14: 0.008288008288008287
20
+ IGHJ1_star_01_15: 0.0072520072520072506
21
+ IGHJ1_star_01_16: 0.006216006216006215
22
+ IGHJ1_star_01_17: 0.005180005180005178
23
+ IGHJ1_star_01_18: 0.004144004144004142
24
+ IGHJ1_star_01_2: 0.011396011396011397
25
+ IGHJ1_star_01_3: 0.011396011396011397
26
+ IGHJ1_star_01_4: 0.011396011396011397
27
+ IGHJ1_star_01_5: 0.011396011396011397
28
+ IGHJ1_star_01_6: 0.011396011396011397
29
+ IGHJ1_star_01_7: 0.011396011396011397
30
+ IGHJ1_star_01_8: 0.011396011396011397
31
+ IGHJ1_star_01_9: 0.011396011396011397
32
+ insert_left_A: 0.17786561264822132
33
+ insert_left_C: 0.2519762845849802
34
+ insert_left_G: 0.18379446640316205
35
+ insert_left_T: 0.20454545454545453
36
+ - !!python/object:python.hmmwriter.State
37
+ emissions:
38
+ probs:
39
+ A: 0.8758141682068817
40
+ C: 0.04139527726437276
41
+ G: 0.04139527726437276
42
+ T: 0.04139527726437276
43
+ track: nukes
44
+ extras:
45
+ ambiguous_char: N
46
+ ambiguous_emission_prob: 0.25
47
+ germline: A
48
+ name: insert_left_A
49
+ transitions:
50
+ IGHJ1_star_01_0: 0.020278196748784987
51
+ IGHJ1_star_01_1: 0.040556393497569974
52
+ IGHJ1_star_01_10: 0.040556393497569974
53
+ IGHJ1_star_01_11: 0.040556393497569974
54
+ IGHJ1_star_01_12: 0.03686944863415452
55
+ IGHJ1_star_01_13: 0.033182503770739065
56
+ IGHJ1_star_01_14: 0.02949555890732361
57
+ IGHJ1_star_01_15: 0.02580861404390816
58
+ IGHJ1_star_01_16: 0.022121669180492708
59
+ IGHJ1_star_01_17: 0.018434724317077253
60
+ IGHJ1_star_01_18: 0.0147477794536618
61
+ IGHJ1_star_01_2: 0.040556393497569974
62
+ IGHJ1_star_01_3: 0.040556393497569974
63
+ IGHJ1_star_01_4: 0.040556393497569974
64
+ IGHJ1_star_01_5: 0.040556393497569974
65
+ IGHJ1_star_01_6: 0.040556393497569974
66
+ IGHJ1_star_01_7: 0.040556393497569974
67
+ IGHJ1_star_01_8: 0.040556393497569974
68
+ IGHJ1_star_01_9: 0.040556393497569974
69
+ insert_left_A: 0.07672634271099743
70
+ insert_left_C: 0.10869565217391303
71
+ insert_left_G: 0.07928388746803068
72
+ insert_left_T: 0.08823529411764705
73
+ - !!python/object:python.hmmwriter.State
74
+ emissions:
75
+ probs:
76
+ A: 0.04139527726437276
77
+ C: 0.8758141682068817
78
+ G: 0.04139527726437276
79
+ T: 0.04139527726437276
80
+ track: nukes
81
+ extras:
82
+ ambiguous_char: N
83
+ ambiguous_emission_prob: 0.25
84
+ germline: C
85
+ name: insert_left_C
86
+ transitions:
87
+ IGHJ1_star_01_0: 0.020278196748784987
88
+ IGHJ1_star_01_1: 0.040556393497569974
89
+ IGHJ1_star_01_10: 0.040556393497569974
90
+ IGHJ1_star_01_11: 0.040556393497569974
91
+ IGHJ1_star_01_12: 0.03686944863415452
92
+ IGHJ1_star_01_13: 0.033182503770739065
93
+ IGHJ1_star_01_14: 0.02949555890732361
94
+ IGHJ1_star_01_15: 0.02580861404390816
95
+ IGHJ1_star_01_16: 0.022121669180492708
96
+ IGHJ1_star_01_17: 0.018434724317077253
97
+ IGHJ1_star_01_18: 0.0147477794536618
98
+ IGHJ1_star_01_2: 0.040556393497569974
99
+ IGHJ1_star_01_3: 0.040556393497569974
100
+ IGHJ1_star_01_4: 0.040556393497569974
101
+ IGHJ1_star_01_5: 0.040556393497569974
102
+ IGHJ1_star_01_6: 0.040556393497569974
103
+ IGHJ1_star_01_7: 0.040556393497569974
104
+ IGHJ1_star_01_8: 0.040556393497569974
105
+ IGHJ1_star_01_9: 0.040556393497569974
106
+ insert_left_A: 0.07672634271099743
107
+ insert_left_C: 0.10869565217391303
108
+ insert_left_G: 0.07928388746803068
109
+ insert_left_T: 0.08823529411764705
110
+ - !!python/object:python.hmmwriter.State
111
+ emissions:
112
+ probs:
113
+ A: 0.04139527726437276
114
+ C: 0.04139527726437276
115
+ G: 0.8758141682068817
116
+ T: 0.04139527726437276
117
+ track: nukes
118
+ extras:
119
+ ambiguous_char: N
120
+ ambiguous_emission_prob: 0.25
121
+ germline: G
122
+ name: insert_left_G
123
+ transitions:
124
+ IGHJ1_star_01_0: 0.020278196748784987
125
+ IGHJ1_star_01_1: 0.040556393497569974
126
+ IGHJ1_star_01_10: 0.040556393497569974
127
+ IGHJ1_star_01_11: 0.040556393497569974
128
+ IGHJ1_star_01_12: 0.03686944863415452
129
+ IGHJ1_star_01_13: 0.033182503770739065
130
+ IGHJ1_star_01_14: 0.02949555890732361
131
+ IGHJ1_star_01_15: 0.02580861404390816
132
+ IGHJ1_star_01_16: 0.022121669180492708
133
+ IGHJ1_star_01_17: 0.018434724317077253
134
+ IGHJ1_star_01_18: 0.0147477794536618
135
+ IGHJ1_star_01_2: 0.040556393497569974
136
+ IGHJ1_star_01_3: 0.040556393497569974
137
+ IGHJ1_star_01_4: 0.040556393497569974
138
+ IGHJ1_star_01_5: 0.040556393497569974
139
+ IGHJ1_star_01_6: 0.040556393497569974
140
+ IGHJ1_star_01_7: 0.040556393497569974
141
+ IGHJ1_star_01_8: 0.040556393497569974
142
+ IGHJ1_star_01_9: 0.040556393497569974
143
+ insert_left_A: 0.07672634271099743
144
+ insert_left_C: 0.10869565217391303
145
+ insert_left_G: 0.07928388746803068
146
+ insert_left_T: 0.08823529411764705
147
+ - !!python/object:python.hmmwriter.State
148
+ emissions:
149
+ probs:
150
+ A: 0.04139527726437276
151
+ C: 0.04139527726437276
152
+ G: 0.04139527726437276
153
+ T: 0.8758141682068817
154
+ track: nukes
155
+ extras:
156
+ ambiguous_char: N
157
+ ambiguous_emission_prob: 0.25
158
+ germline: T
159
+ name: insert_left_T
160
+ transitions:
161
+ IGHJ1_star_01_0: 0.020278196748784987
162
+ IGHJ1_star_01_1: 0.040556393497569974
163
+ IGHJ1_star_01_10: 0.040556393497569974
164
+ IGHJ1_star_01_11: 0.040556393497569974
165
+ IGHJ1_star_01_12: 0.03686944863415452
166
+ IGHJ1_star_01_13: 0.033182503770739065
167
+ IGHJ1_star_01_14: 0.02949555890732361
168
+ IGHJ1_star_01_15: 0.02580861404390816
169
+ IGHJ1_star_01_16: 0.022121669180492708
170
+ IGHJ1_star_01_17: 0.018434724317077253
171
+ IGHJ1_star_01_18: 0.0147477794536618
172
+ IGHJ1_star_01_2: 0.040556393497569974
173
+ IGHJ1_star_01_3: 0.040556393497569974
174
+ IGHJ1_star_01_4: 0.040556393497569974
175
+ IGHJ1_star_01_5: 0.040556393497569974
176
+ IGHJ1_star_01_6: 0.040556393497569974
177
+ IGHJ1_star_01_7: 0.040556393497569974
178
+ IGHJ1_star_01_8: 0.040556393497569974
179
+ IGHJ1_star_01_9: 0.040556393497569974
180
+ insert_left_A: 0.07672634271099743
181
+ insert_left_C: 0.10869565217391303
182
+ insert_left_G: 0.07928388746803068
183
+ insert_left_T: 0.08823529411764705
184
+ - !!python/object:python.hmmwriter.State
185
+ emissions:
186
+ probs:
187
+ A: 0.04139527726437276
188
+ C: 0.04139527726437276
189
+ G: 0.8758141682068817
190
+ T: 0.04139527726437276
191
+ track: nukes
192
+ extras:
193
+ ambiguous_char: N
194
+ ambiguous_emission_prob: 0.25
195
+ germline: G
196
+ name: IGHJ1_star_01_0
197
+ transitions:
198
+ IGHJ1_star_01_1: 1.0
199
+ - !!python/object:python.hmmwriter.State
200
+ emissions:
201
+ probs:
202
+ A: 0.04122693170991329
203
+ C: 0.8763192048702602
204
+ G: 0.04122693170991329
205
+ T: 0.04122693170991329
206
+ track: nukes
207
+ extras:
208
+ ambiguous_char: N
209
+ ambiguous_emission_prob: 0.25
210
+ germline: C
211
+ name: IGHJ1_star_01_1
212
+ transitions:
213
+ IGHJ1_star_01_2: 1.0
214
+ - !!python/object:python.hmmwriter.State
215
+ emissions:
216
+ probs:
217
+ A: 0.04142241620460216
218
+ C: 0.04142241620460216
219
+ G: 0.04142241620460216
220
+ T: 0.8757327513861936
221
+ track: nukes
222
+ extras:
223
+ ambiguous_char: N
224
+ ambiguous_emission_prob: 0.25
225
+ germline: T
226
+ name: IGHJ1_star_01_2
227
+ transitions:
228
+ IGHJ1_star_01_3: 1.0
229
+ - !!python/object:python.hmmwriter.State
230
+ emissions:
231
+ probs:
232
+ A: 0.040890240600994346
233
+ C: 0.040890240600994346
234
+ G: 0.877329278197017
235
+ T: 0.040890240600994346
236
+ track: nukes
237
+ extras:
238
+ ambiguous_char: N
239
+ ambiguous_emission_prob: 0.25
240
+ germline: G
241
+ name: IGHJ1_star_01_3
242
+ transitions:
243
+ IGHJ1_star_01_4: 1.0
244
+ - !!python/object:python.hmmwriter.State
245
+ emissions:
246
+ probs:
247
+ A: 0.8756513345655054
248
+ C: 0.04144955514483154
249
+ G: 0.04144955514483154
250
+ T: 0.04144955514483154
251
+ track: nukes
252
+ extras:
253
+ ambiguous_char: N
254
+ ambiguous_emission_prob: 0.25
255
+ germline: A
256
+ name: IGHJ1_star_01_4
257
+ transitions:
258
+ IGHJ1_star_01_5: 1.0
259
+ - !!python/object:python.hmmwriter.State
260
+ emissions:
261
+ probs:
262
+ A: 0.8756106261551613
263
+ C: 0.04146312461494624
264
+ G: 0.04146312461494624
265
+ T: 0.04146312461494624
266
+ track: nukes
267
+ extras:
268
+ ambiguous_char: N
269
+ ambiguous_emission_prob: 0.25
270
+ germline: A
271
+ name: IGHJ1_star_01_5
272
+ transitions:
273
+ IGHJ1_star_01_6: 1.0
274
+ - !!python/object:python.hmmwriter.State
275
+ emissions:
276
+ probs:
277
+ A: 0.04038520393761593
278
+ C: 0.04038520393761593
279
+ G: 0.04038520393761593
280
+ T: 0.8788443881871522
281
+ track: nukes
282
+ extras:
283
+ ambiguous_char: N
284
+ ambiguous_emission_prob: 0.25
285
+ germline: T
286
+ name: IGHJ1_star_01_6
287
+ transitions:
288
+ IGHJ1_star_01_7: 1.0
289
+ - !!python/object:python.hmmwriter.State
290
+ emissions:
291
+ probs:
292
+ A: 0.8755292093344731
293
+ C: 0.04149026355517563
294
+ G: 0.04149026355517563
295
+ T: 0.04149026355517563
296
+ track: nukes
297
+ extras:
298
+ ambiguous_char: N
299
+ ambiguous_emission_prob: 0.25
300
+ germline: A
301
+ name: IGHJ1_star_01_7
302
+ transitions:
303
+ IGHJ1_star_01_8: 1.0
304
+ - !!python/object:python.hmmwriter.State
305
+ emissions:
306
+ probs:
307
+ A: 0.04004851282869699
308
+ C: 0.879854461513909
309
+ G: 0.04004851282869699
310
+ T: 0.04004851282869699
311
+ track: nukes
312
+ extras:
313
+ ambiguous_char: N
314
+ ambiguous_emission_prob: 0.25
315
+ germline: C
316
+ name: IGHJ1_star_01_8
317
+ transitions:
318
+ IGHJ1_star_01_9: 1.0
319
+ - !!python/object:python.hmmwriter.State
320
+ emissions:
321
+ probs:
322
+ A: 0.04151740249540502
323
+ C: 0.04151740249540502
324
+ G: 0.04151740249540502
325
+ T: 0.8754477925137849
326
+ track: nukes
327
+ extras:
328
+ ambiguous_char: N
329
+ ambiguous_emission_prob: 0.25
330
+ germline: T
331
+ name: IGHJ1_star_01_9
332
+ transitions:
333
+ IGHJ1_star_01_10: 1.0
334
+ - !!python/object:python.hmmwriter.State
335
+ emissions:
336
+ probs:
337
+ A: 0.03971182171977805
338
+ C: 0.03971182171977805
339
+ G: 0.03971182171977805
340
+ T: 0.8808645348406658
341
+ track: nukes
342
+ extras:
343
+ ambiguous_char: N
344
+ ambiguous_emission_prob: 0.25
345
+ germline: T
346
+ name: IGHJ1_star_01_10
347
+ transitions:
348
+ IGHJ1_star_01_11: 1.0
349
+ - !!python/object:python.hmmwriter.State
350
+ emissions:
351
+ probs:
352
+ A: 0.042461208102301085
353
+ C: 0.8726163756930967
354
+ G: 0.042461208102301085
355
+ T: 0.042461208102301085
356
+ track: nukes
357
+ extras:
358
+ ambiguous_char: N
359
+ ambiguous_emission_prob: 0.25
360
+ germline: C
361
+ name: IGHJ1_star_01_11
362
+ transitions:
363
+ IGHJ1_star_01_12: 1.0
364
+ - !!python/object:python.hmmwriter.State
365
+ emissions:
366
+ probs:
367
+ A: 0.042558110905749104
368
+ C: 0.8723256672827526
369
+ G: 0.042558110905749104
370
+ T: 0.042558110905749104
371
+ track: nukes
372
+ extras:
373
+ ambiguous_char: N
374
+ ambiguous_emission_prob: 0.25
375
+ germline: C
376
+ name: IGHJ1_star_01_12
377
+ transitions:
378
+ IGHJ1_star_01_13: 1.0
379
+ - !!python/object:python.hmmwriter.State
380
+ emissions:
381
+ probs:
382
+ A: 0.8590349588724087
383
+ C: 0.02819300822551828
384
+ G: 0.02819300822551828
385
+ T: 0.08457902467655483
386
+ track: nukes
387
+ extras:
388
+ ambiguous_char: N
389
+ ambiguous_emission_prob: 0.25
390
+ germline: A
391
+ name: IGHJ1_star_01_13
392
+ transitions:
393
+ IGHJ1_star_01_14: 1.0
394
+ - !!python/object:python.hmmwriter.State
395
+ emissions:
396
+ probs:
397
+ A: 0.039630973338671834
398
+ C: 0.039630973338671834
399
+ G: 0.8811070799839845
400
+ T: 0.039630973338671834
401
+ track: nukes
402
+ extras:
403
+ ambiguous_char: N
404
+ ambiguous_emission_prob: 0.25
405
+ germline: G
406
+ name: IGHJ1_star_01_14
407
+ transitions:
408
+ IGHJ1_star_01_15: 1.0
409
+ - !!python/object:python.hmmwriter.State
410
+ emissions:
411
+ probs:
412
+ A: 0.03588661448706989
413
+ C: 0.8564535420517204
414
+ G: 0.03588661448706989
415
+ T: 0.07177322897413978
416
+ track: nukes
417
+ extras:
418
+ ambiguous_char: N
419
+ ambiguous_emission_prob: 0.25
420
+ germline: C
421
+ name: IGHJ1_star_01_15
422
+ transitions:
423
+ IGHJ1_star_01_16: 1.0
424
+ - !!python/object:python.hmmwriter.State
425
+ emissions:
426
+ probs:
427
+ A: 0.8711628336413764
428
+ C: 0.042945722119541216
429
+ G: 0.042945722119541216
430
+ T: 0.042945722119541216
431
+ track: nukes
432
+ extras:
433
+ ambiguous_char: N
434
+ ambiguous_emission_prob: 0.25
435
+ germline: A
436
+ name: IGHJ1_star_01_16
437
+ transitions:
438
+ IGHJ1_star_01_17: 1.0
439
+ - !!python/object:python.hmmwriter.State
440
+ emissions:
441
+ probs:
442
+ A: 0.04304262492298925
443
+ C: 0.8708721252310323
444
+ G: 0.04304262492298925
445
+ T: 0.04304262492298925
446
+ track: nukes
447
+ extras:
448
+ ambiguous_char: N
449
+ ambiguous_emission_prob: 0.25
450
+ germline: C
451
+ name: IGHJ1_star_01_17
452
+ transitions:
453
+ IGHJ1_star_01_18: 1.0
454
+ - !!python/object:python.hmmwriter.State
455
+ emissions:
456
+ probs:
457
+ A: 0.03912688650275728
458
+ C: 0.03912688650275728
459
+ G: 0.03912688650275728
460
+ T: 0.8826193404917282
461
+ track: nukes
462
+ extras:
463
+ ambiguous_char: N
464
+ ambiguous_emission_prob: 0.25
465
+ germline: T
466
+ name: IGHJ1_star_01_18
467
+ transitions:
468
+ IGHJ1_star_01_19: 1.0
469
+ - !!python/object:python.hmmwriter.State
470
+ emissions:
471
+ probs:
472
+ A: 0.039000864793778636
473
+ C: 0.039000864793778636
474
+ G: 0.8829974056186641
475
+ T: 0.039000864793778636
476
+ track: nukes
477
+ extras:
478
+ ambiguous_char: N
479
+ ambiguous_emission_prob: 0.25
480
+ germline: G
481
+ name: IGHJ1_star_01_19
482
+ transitions:
483
+ IGHJ1_star_01_20: 1.0
484
+ - !!python/object:python.hmmwriter.State
485
+ emissions:
486
+ probs:
487
+ A: 0.0388748430848
488
+ C: 0.0388748430848
489
+ G: 0.8833754707456
490
+ T: 0.0388748430848
491
+ track: nukes
492
+ extras:
493
+ ambiguous_char: N
494
+ ambiguous_emission_prob: 0.25
495
+ germline: G
496
+ name: IGHJ1_star_01_20
497
+ transitions:
498
+ IGHJ1_star_01_21: 1.0
499
+ - !!python/object:python.hmmwriter.State
500
+ emissions:
501
+ probs:
502
+ A: 0.0388748430848
503
+ C: 0.0388748430848
504
+ G: 0.8833754707456
505
+ T: 0.0388748430848
506
+ track: nukes
507
+ extras:
508
+ ambiguous_char: N
509
+ ambiguous_emission_prob: 0.25
510
+ germline: G
511
+ name: IGHJ1_star_01_21
512
+ transitions:
513
+ IGHJ1_star_01_22: 1.0
514
+ - !!python/object:python.hmmwriter.State
515
+ emissions:
516
+ probs:
517
+ A: 0.0388748430848
518
+ C: 0.0388748430848
519
+ G: 0.8833754707456
520
+ T: 0.0388748430848
521
+ track: nukes
522
+ extras:
523
+ ambiguous_char: N
524
+ ambiguous_emission_prob: 0.25
525
+ germline: G
526
+ name: IGHJ1_star_01_22
527
+ transitions:
528
+ IGHJ1_star_01_23: 1.0
529
+ - !!python/object:python.hmmwriter.State
530
+ emissions:
531
+ probs:
532
+ A: 0.09
533
+ C: 0.85
534
+ G: 0.03
535
+ T: 0.03
536
+ track: nukes
537
+ extras:
538
+ ambiguous_char: N
539
+ ambiguous_emission_prob: 0.25
540
+ germline: C
541
+ name: IGHJ1_star_01_23
542
+ transitions:
543
+ IGHJ1_star_01_24: 1.0
544
+ - !!python/object:python.hmmwriter.State
545
+ emissions:
546
+ probs:
547
+ A: 0.0388748430848
548
+ C: 0.8833754707456
549
+ G: 0.0388748430848
550
+ T: 0.0388748430848
551
+ track: nukes
552
+ extras:
553
+ ambiguous_char: N
554
+ ambiguous_emission_prob: 0.25
555
+ germline: C
556
+ name: IGHJ1_star_01_24
557
+ transitions:
558
+ IGHJ1_star_01_25: 1.0
559
+ - !!python/object:python.hmmwriter.State
560
+ emissions:
561
+ probs:
562
+ A: 0.8833754707456
563
+ C: 0.0388748430848
564
+ G: 0.0388748430848
565
+ T: 0.0388748430848
566
+ track: nukes
567
+ extras:
568
+ ambiguous_char: N
569
+ ambiguous_emission_prob: 0.25
570
+ germline: A
571
+ name: IGHJ1_star_01_25
572
+ transitions:
573
+ IGHJ1_star_01_26: 1.0
574
+ - !!python/object:python.hmmwriter.State
575
+ emissions:
576
+ probs:
577
+ A: 0.0388748430848
578
+ C: 0.0388748430848
579
+ G: 0.8833754707456
580
+ T: 0.0388748430848
581
+ track: nukes
582
+ extras:
583
+ ambiguous_char: N
584
+ ambiguous_emission_prob: 0.25
585
+ germline: G
586
+ name: IGHJ1_star_01_26
587
+ transitions:
588
+ IGHJ1_star_01_27: 1.0
589
+ - !!python/object:python.hmmwriter.State
590
+ emissions:
591
+ probs:
592
+ A: 0.0388748430848
593
+ C: 0.0388748430848
594
+ G: 0.8833754707456
595
+ T: 0.0388748430848
596
+ track: nukes
597
+ extras:
598
+ ambiguous_char: N
599
+ ambiguous_emission_prob: 0.25
600
+ germline: G
601
+ name: IGHJ1_star_01_27
602
+ transitions:
603
+ IGHJ1_star_01_28: 1.0
604
+ - !!python/object:python.hmmwriter.State
605
+ emissions:
606
+ probs:
607
+ A: 0.0388748430848
608
+ C: 0.0388748430848
609
+ G: 0.8833754707456
610
+ T: 0.0388748430848
611
+ track: nukes
612
+ extras:
613
+ ambiguous_char: N
614
+ ambiguous_emission_prob: 0.25
615
+ germline: G
616
+ name: IGHJ1_star_01_28
617
+ transitions:
618
+ IGHJ1_star_01_29: 1.0
619
+ - !!python/object:python.hmmwriter.State
620
+ emissions:
621
+ probs:
622
+ A: 0.03
623
+ C: 0.85
624
+ G: 0.09
625
+ T: 0.03
626
+ track: nukes
627
+ extras:
628
+ ambiguous_char: N
629
+ ambiguous_emission_prob: 0.25
630
+ germline: C
631
+ name: IGHJ1_star_01_29
632
+ transitions:
633
+ IGHJ1_star_01_30: 1.0
634
+ - !!python/object:python.hmmwriter.State
635
+ emissions:
636
+ probs:
637
+ A: 0.8833754707456
638
+ C: 0.0388748430848
639
+ G: 0.0388748430848
640
+ T: 0.0388748430848
641
+ track: nukes
642
+ extras:
643
+ ambiguous_char: N
644
+ ambiguous_emission_prob: 0.25
645
+ germline: A
646
+ name: IGHJ1_star_01_30
647
+ transitions:
648
+ IGHJ1_star_01_31: 1.0
649
+ - !!python/object:python.hmmwriter.State
650
+ emissions:
651
+ probs:
652
+ A: 0.0375
653
+ C: 0.85
654
+ G: 0.0375
655
+ T: 0.075
656
+ track: nukes
657
+ extras:
658
+ ambiguous_char: N
659
+ ambiguous_emission_prob: 0.25
660
+ germline: C
661
+ name: IGHJ1_star_01_31
662
+ transitions:
663
+ IGHJ1_star_01_32: 1.0
664
+ - !!python/object:python.hmmwriter.State
665
+ emissions:
666
+ probs:
667
+ A: 0.0375
668
+ C: 0.85
669
+ G: 0.0375
670
+ T: 0.075
671
+ track: nukes
672
+ extras:
673
+ ambiguous_char: N
674
+ ambiguous_emission_prob: 0.25
675
+ germline: C
676
+ name: IGHJ1_star_01_32
677
+ transitions:
678
+ IGHJ1_star_01_33: 1.0
679
+ - !!python/object:python.hmmwriter.State
680
+ emissions:
681
+ probs:
682
+ A: 0.0388748430848
683
+ C: 0.8833754707456
684
+ G: 0.0388748430848
685
+ T: 0.0388748430848
686
+ track: nukes
687
+ extras:
688
+ ambiguous_char: N
689
+ ambiguous_emission_prob: 0.25
690
+ germline: C
691
+ name: IGHJ1_star_01_33
692
+ transitions:
693
+ IGHJ1_star_01_34: 1.0
694
+ - !!python/object:python.hmmwriter.State
695
+ emissions:
696
+ probs:
697
+ A: 0.043333333333333335
698
+ C: 0.043333333333333335
699
+ G: 0.043333333333333335
700
+ T: 0.87
701
+ track: nukes
702
+ extras:
703
+ ambiguous_char: N
704
+ ambiguous_emission_prob: 0.25
705
+ germline: T
706
+ name: IGHJ1_star_01_34
707
+ transitions:
708
+ IGHJ1_star_01_35: 1.0
709
+ - !!python/object:python.hmmwriter.State
710
+ emissions:
711
+ probs:
712
+ A: 0.0388748430848
713
+ C: 0.0388748430848
714
+ G: 0.8833754707456
715
+ T: 0.0388748430848
716
+ track: nukes
717
+ extras:
718
+ ambiguous_char: N
719
+ ambiguous_emission_prob: 0.25
720
+ germline: G
721
+ name: IGHJ1_star_01_35
722
+ transitions:
723
+ IGHJ1_star_01_36: 1.0
724
+ - !!python/object:python.hmmwriter.State
725
+ emissions:
726
+ probs:
727
+ A: 0.0388748430848
728
+ C: 0.0388748430848
729
+ G: 0.8833754707456
730
+ T: 0.0388748430848
731
+ track: nukes
732
+ extras:
733
+ ambiguous_char: N
734
+ ambiguous_emission_prob: 0.25
735
+ germline: G
736
+ name: IGHJ1_star_01_36
737
+ transitions:
738
+ IGHJ1_star_01_37: 1.0
739
+ - !!python/object:python.hmmwriter.State
740
+ emissions:
741
+ probs:
742
+ A: 0.0388748430848
743
+ C: 0.0388748430848
744
+ G: 0.0388748430848
745
+ T: 0.8833754707456
746
+ track: nukes
747
+ extras:
748
+ ambiguous_char: N
749
+ ambiguous_emission_prob: 0.25
750
+ germline: T
751
+ name: IGHJ1_star_01_37
752
+ transitions:
753
+ IGHJ1_star_01_38: 1.0
754
+ - !!python/object:python.hmmwriter.State
755
+ emissions:
756
+ probs:
757
+ A: 0.0388748430848
758
+ C: 0.8833754707456
759
+ G: 0.0388748430848
760
+ T: 0.0388748430848
761
+ track: nukes
762
+ extras:
763
+ ambiguous_char: N
764
+ ambiguous_emission_prob: 0.25
765
+ germline: C
766
+ name: IGHJ1_star_01_38
767
+ transitions:
768
+ IGHJ1_star_01_39: 1.0
769
+ - !!python/object:python.hmmwriter.State
770
+ emissions:
771
+ probs:
772
+ A: 0.85
773
+ C: 0.0375
774
+ G: 0.0375
775
+ T: 0.075
776
+ track: nukes
777
+ extras:
778
+ ambiguous_char: N
779
+ ambiguous_emission_prob: 0.25
780
+ germline: A
781
+ name: IGHJ1_star_01_39
782
+ transitions:
783
+ IGHJ1_star_01_40: 1.0
784
+ - !!python/object:python.hmmwriter.State
785
+ emissions:
786
+ probs:
787
+ A: 0.0375
788
+ C: 0.85
789
+ G: 0.0375
790
+ T: 0.075
791
+ track: nukes
792
+ extras:
793
+ ambiguous_char: N
794
+ ambiguous_emission_prob: 0.25
795
+ germline: C
796
+ name: IGHJ1_star_01_40
797
+ transitions:
798
+ IGHJ1_star_01_41: 1.0
799
+ - !!python/object:python.hmmwriter.State
800
+ emissions:
801
+ probs:
802
+ A: 0.0388748430848
803
+ C: 0.8833754707456
804
+ G: 0.0388748430848
805
+ T: 0.0388748430848
806
+ track: nukes
807
+ extras:
808
+ ambiguous_char: N
809
+ ambiguous_emission_prob: 0.25
810
+ germline: C
811
+ name: IGHJ1_star_01_41
812
+ transitions:
813
+ IGHJ1_star_01_42: 1.0
814
+ - !!python/object:python.hmmwriter.State
815
+ emissions:
816
+ probs:
817
+ A: 0.0388748430848
818
+ C: 0.0388748430848
819
+ G: 0.8833754707456
820
+ T: 0.0388748430848
821
+ track: nukes
822
+ extras:
823
+ ambiguous_char: N
824
+ ambiguous_emission_prob: 0.25
825
+ germline: G
826
+ name: IGHJ1_star_01_42
827
+ transitions:
828
+ IGHJ1_star_01_43: 1.0
829
+ - !!python/object:python.hmmwriter.State
830
+ emissions:
831
+ probs:
832
+ A: 0.0388748430848
833
+ C: 0.0388748430848
834
+ G: 0.0388748430848
835
+ T: 0.8833754707456
836
+ track: nukes
837
+ extras:
838
+ ambiguous_char: N
839
+ ambiguous_emission_prob: 0.25
840
+ germline: T
841
+ name: IGHJ1_star_01_43
842
+ transitions:
843
+ IGHJ1_star_01_44: 1.0
844
+ - !!python/object:python.hmmwriter.State
845
+ emissions:
846
+ probs:
847
+ A: 0.0388748430848
848
+ C: 0.8833754707456
849
+ G: 0.0388748430848
850
+ T: 0.0388748430848
851
+ track: nukes
852
+ extras:
853
+ ambiguous_char: N
854
+ ambiguous_emission_prob: 0.25
855
+ germline: C
856
+ name: IGHJ1_star_01_44
857
+ transitions:
858
+ IGHJ1_star_01_45: 1.0
859
+ - !!python/object:python.hmmwriter.State
860
+ emissions:
861
+ probs:
862
+ A: 0.0388748430848
863
+ C: 0.0388748430848
864
+ G: 0.0388748430848
865
+ T: 0.8833754707456
866
+ track: nukes
867
+ extras:
868
+ ambiguous_char: N
869
+ ambiguous_emission_prob: 0.25
870
+ germline: T
871
+ name: IGHJ1_star_01_45
872
+ transitions:
873
+ IGHJ1_star_01_46: 1.0
874
+ - !!python/object:python.hmmwriter.State
875
+ emissions:
876
+ probs:
877
+ A: 0.043333333333333335
878
+ C: 0.87
879
+ G: 0.043333333333333335
880
+ T: 0.043333333333333335
881
+ track: nukes
882
+ extras:
883
+ ambiguous_char: N
884
+ ambiguous_emission_prob: 0.25
885
+ germline: C
886
+ name: IGHJ1_star_01_46
887
+ transitions:
888
+ IGHJ1_star_01_47: 1.0
889
+ - !!python/object:python.hmmwriter.State
890
+ emissions:
891
+ probs:
892
+ A: 0.03
893
+ C: 0.85
894
+ G: 0.03
895
+ T: 0.09
896
+ track: nukes
897
+ extras:
898
+ ambiguous_char: N
899
+ ambiguous_emission_prob: 0.25
900
+ germline: C
901
+ name: IGHJ1_star_01_47
902
+ transitions:
903
+ IGHJ1_star_01_48: 1.0
904
+ - !!python/object:python.hmmwriter.State
905
+ emissions:
906
+ probs:
907
+ A: 0.0388748430848
908
+ C: 0.0388748430848
909
+ G: 0.0388748430848
910
+ T: 0.8833754707456
911
+ track: nukes
912
+ extras:
913
+ ambiguous_char: N
914
+ ambiguous_emission_prob: 0.25
915
+ germline: T
916
+ name: IGHJ1_star_01_48
917
+ transitions:
918
+ IGHJ1_star_01_49: 1.0
919
+ - !!python/object:python.hmmwriter.State
920
+ emissions:
921
+ probs:
922
+ A: 0.0388748430848
923
+ C: 0.8833754707456
924
+ G: 0.0388748430848
925
+ T: 0.0388748430848
926
+ track: nukes
927
+ extras:
928
+ ambiguous_char: N
929
+ ambiguous_emission_prob: 0.25
930
+ germline: C
931
+ name: IGHJ1_star_01_49
932
+ transitions:
933
+ IGHJ1_star_01_50: 1.0
934
+ - !!python/object:python.hmmwriter.State
935
+ emissions:
936
+ probs:
937
+ A: 0.8833754707456
938
+ C: 0.0388748430848
939
+ G: 0.0388748430848
940
+ T: 0.0388748430848
941
+ track: nukes
942
+ extras:
943
+ ambiguous_char: N
944
+ ambiguous_emission_prob: 0.25
945
+ germline: A
946
+ name: IGHJ1_star_01_50
947
+ transitions:
948
+ IGHJ1_star_01_51: 1.0
949
+ - !!python/object:python.hmmwriter.State
950
+ emissions:
951
+ probs:
952
+ A: 0.0388748430848
953
+ C: 0.0388748430848
954
+ G: 0.8833754707456
955
+ T: 0.0388748430848
956
+ track: nukes
957
+ extras:
958
+ ambiguous_char: N
959
+ ambiguous_emission_prob: 0.25
960
+ germline: G
961
+ name: IGHJ1_star_01_51
962
+ transitions:
963
+ end: 0.04
964
+ insert_right_N: 0.96
965
+ - !!python/object:python.hmmwriter.State
966
+ emissions:
967
+ probs:
968
+ A: 0.25
969
+ C: 0.25
970
+ G: 0.25
971
+ T: 0.25
972
+ track: nukes
973
+ extras:
974
+ ambiguous_char: N
975
+ ambiguous_emission_prob: 0.25
976
+ germline: N
977
+ name: insert_right_N
978
+ transitions:
979
+ end: 0.040000000000000036
980
+ insert_right_N: 0.96
981
+ tracks:
982
+ nukes:
983
+ - A
984
+ - C
985
+ - G
986
+ - T