partis-bcr 1.0.11.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl → 1.0.11.post1.dev7__cp312-cp312-macosx_10_13_universal2.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (645) 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.dev7.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +645 -127
  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 +9 -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.log +203 -24
  604. test/new-results/vsearch-partition-new-simu.yaml +1 -0
  605. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  606. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +5 -5
  607. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +2 -2
  608. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +1 -1
  609. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  610. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  611. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  612. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  613. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  614. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  615. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  616. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  617. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  618. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  619. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  620. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  621. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  622. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  623. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  624. test/paired/new-results/run-times.csv +6 -6
  625. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +43 -43
  626. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +40 -40
  627. test/paired/new-results/subset-partition-new-simu/merged-partition.log +25 -25
  628. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  629. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  630. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  631. test/paired/new-results/test.log +135 -135
  632. test/test.py +6 -0
  633. test/trees.nwk +100 -0
  634. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  635. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  636. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  637. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  638. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  639. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  640. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/data/hmm/hmms/IGHD6-13_star_01.yaml ADDED
@@ -0,0 +1,533 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.21739130434782608
4
+ overall_mute_freq: 0.08760869565217394
5
+ per_gene_mute_freq: 0.12622187310705474
6
+ name: IGHD6-13_star_01
7
+ states:
8
+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
11
+ name: init
12
+ transitions:
13
+ IGHD6-13_star_01_0: 0.0037593984962406013
14
+ IGHD6-13_star_01_1: 0.0037593984962406013
15
+ IGHD6-13_star_01_10: 0.003341687552213868
16
+ IGHD6-13_star_01_11: 0.0029239766081871343
17
+ IGHD6-13_star_01_12: 0.0025062656641604004
18
+ IGHD6-13_star_01_13: 0.0020885547201336665
19
+ IGHD6-13_star_01_14: 0.001670843776106933
20
+ IGHD6-13_star_01_15: 0.0012531328320801996
21
+ IGHD6-13_star_01_16: 0.0008354218880534663
22
+ IGHD6-13_star_01_17: 0.0004177109440267328
23
+ IGHD6-13_star_01_18: 0.0037593984962406013
24
+ IGHD6-13_star_01_19: 0.0037593984962406013
25
+ IGHD6-13_star_01_2: 0.0037593984962406013
26
+ IGHD6-13_star_01_20: 0.0037593984962406013
27
+ IGHD6-13_star_01_3: 0.007518796992481203
28
+ IGHD6-13_star_01_4: 0.007518796992481203
29
+ IGHD6-13_star_01_5: 0.0037593984962406013
30
+ IGHD6-13_star_01_6: 0.0037593984962406013
31
+ IGHD6-13_star_01_7: 0.0037593984962406013
32
+ IGHD6-13_star_01_8: 0.0037593984962406013
33
+ IGHD6-13_star_01_9: 0.0037593984962406013
34
+ insert_left_A: 0.17454350161117077
35
+ insert_left_C: 0.3141783029001074
36
+ insert_left_G: 0.21643394199785176
37
+ insert_left_T: 0.2234156820622986
38
+ - !!python/object:python.hmmwriter.State
39
+ emissions:
40
+ probs:
41
+ A: 0.8737781268929452
42
+ C: 0.04207395770235158
43
+ G: 0.04207395770235158
44
+ T: 0.04207395770235158
45
+ track: nukes
46
+ extras:
47
+ ambiguous_char: N
48
+ ambiguous_emission_prob: 0.25
49
+ germline: A
50
+ name: insert_left_A
51
+ transitions:
52
+ IGHD6-13_star_01_0: 0.009738001391143055
53
+ IGHD6-13_star_01_1: 0.009738001391143055
54
+ IGHD6-13_star_01_10: 0.008656001236571604
55
+ IGHD6-13_star_01_11: 0.0075740010820001535
56
+ IGHD6-13_star_01_12: 0.006492000927428702
57
+ IGHD6-13_star_01_13: 0.005410000772857251
58
+ IGHD6-13_star_01_14: 0.0043280006182858
59
+ IGHD6-13_star_01_15: 0.0032460004637143497
60
+ IGHD6-13_star_01_16: 0.0021640003091428993
61
+ IGHD6-13_star_01_17: 0.001082000154571449
62
+ IGHD6-13_star_01_18: 0.009738001391143055
63
+ IGHD6-13_star_01_19: 0.009738001391143055
64
+ IGHD6-13_star_01_2: 0.009738001391143055
65
+ IGHD6-13_star_01_20: 0.009738001391143055
66
+ IGHD6-13_star_01_3: 0.01947600278228611
67
+ IGHD6-13_star_01_4: 0.01947600278228611
68
+ IGHD6-13_star_01_5: 0.009738001391143055
69
+ IGHD6-13_star_01_6: 0.009738001391143055
70
+ IGHD6-13_star_01_7: 0.009738001391143055
71
+ IGHD6-13_star_01_8: 0.009738001391143055
72
+ IGHD6-13_star_01_9: 0.009738001391143055
73
+ insert_left_A: 0.15319134841509058
74
+ insert_left_C: 0.2757444271471631
75
+ insert_left_G: 0.18995727203471233
76
+ insert_left_T: 0.19608492597131594
77
+ - !!python/object:python.hmmwriter.State
78
+ emissions:
79
+ probs:
80
+ A: 0.04207395770235158
81
+ C: 0.8737781268929452
82
+ G: 0.04207395770235158
83
+ T: 0.04207395770235158
84
+ track: nukes
85
+ extras:
86
+ ambiguous_char: N
87
+ ambiguous_emission_prob: 0.25
88
+ germline: C
89
+ name: insert_left_C
90
+ transitions:
91
+ IGHD6-13_star_01_0: 0.009738001391143055
92
+ IGHD6-13_star_01_1: 0.009738001391143055
93
+ IGHD6-13_star_01_10: 0.008656001236571604
94
+ IGHD6-13_star_01_11: 0.0075740010820001535
95
+ IGHD6-13_star_01_12: 0.006492000927428702
96
+ IGHD6-13_star_01_13: 0.005410000772857251
97
+ IGHD6-13_star_01_14: 0.0043280006182858
98
+ IGHD6-13_star_01_15: 0.0032460004637143497
99
+ IGHD6-13_star_01_16: 0.0021640003091428993
100
+ IGHD6-13_star_01_17: 0.001082000154571449
101
+ IGHD6-13_star_01_18: 0.009738001391143055
102
+ IGHD6-13_star_01_19: 0.009738001391143055
103
+ IGHD6-13_star_01_2: 0.009738001391143055
104
+ IGHD6-13_star_01_20: 0.009738001391143055
105
+ IGHD6-13_star_01_3: 0.01947600278228611
106
+ IGHD6-13_star_01_4: 0.01947600278228611
107
+ IGHD6-13_star_01_5: 0.009738001391143055
108
+ IGHD6-13_star_01_6: 0.009738001391143055
109
+ IGHD6-13_star_01_7: 0.009738001391143055
110
+ IGHD6-13_star_01_8: 0.009738001391143055
111
+ IGHD6-13_star_01_9: 0.009738001391143055
112
+ insert_left_A: 0.15319134841509058
113
+ insert_left_C: 0.2757444271471631
114
+ insert_left_G: 0.18995727203471233
115
+ insert_left_T: 0.19608492597131594
116
+ - !!python/object:python.hmmwriter.State
117
+ emissions:
118
+ probs:
119
+ A: 0.04207395770235158
120
+ C: 0.04207395770235158
121
+ G: 0.8737781268929452
122
+ T: 0.04207395770235158
123
+ track: nukes
124
+ extras:
125
+ ambiguous_char: N
126
+ ambiguous_emission_prob: 0.25
127
+ germline: G
128
+ name: insert_left_G
129
+ transitions:
130
+ IGHD6-13_star_01_0: 0.009738001391143055
131
+ IGHD6-13_star_01_1: 0.009738001391143055
132
+ IGHD6-13_star_01_10: 0.008656001236571604
133
+ IGHD6-13_star_01_11: 0.0075740010820001535
134
+ IGHD6-13_star_01_12: 0.006492000927428702
135
+ IGHD6-13_star_01_13: 0.005410000772857251
136
+ IGHD6-13_star_01_14: 0.0043280006182858
137
+ IGHD6-13_star_01_15: 0.0032460004637143497
138
+ IGHD6-13_star_01_16: 0.0021640003091428993
139
+ IGHD6-13_star_01_17: 0.001082000154571449
140
+ IGHD6-13_star_01_18: 0.009738001391143055
141
+ IGHD6-13_star_01_19: 0.009738001391143055
142
+ IGHD6-13_star_01_2: 0.009738001391143055
143
+ IGHD6-13_star_01_20: 0.009738001391143055
144
+ IGHD6-13_star_01_3: 0.01947600278228611
145
+ IGHD6-13_star_01_4: 0.01947600278228611
146
+ IGHD6-13_star_01_5: 0.009738001391143055
147
+ IGHD6-13_star_01_6: 0.009738001391143055
148
+ IGHD6-13_star_01_7: 0.009738001391143055
149
+ IGHD6-13_star_01_8: 0.009738001391143055
150
+ IGHD6-13_star_01_9: 0.009738001391143055
151
+ insert_left_A: 0.15319134841509058
152
+ insert_left_C: 0.2757444271471631
153
+ insert_left_G: 0.18995727203471233
154
+ insert_left_T: 0.19608492597131594
155
+ - !!python/object:python.hmmwriter.State
156
+ emissions:
157
+ probs:
158
+ A: 0.04207395770235158
159
+ C: 0.04207395770235158
160
+ G: 0.04207395770235158
161
+ T: 0.8737781268929452
162
+ track: nukes
163
+ extras:
164
+ ambiguous_char: N
165
+ ambiguous_emission_prob: 0.25
166
+ germline: T
167
+ name: insert_left_T
168
+ transitions:
169
+ IGHD6-13_star_01_0: 0.009738001391143055
170
+ IGHD6-13_star_01_1: 0.009738001391143055
171
+ IGHD6-13_star_01_10: 0.008656001236571604
172
+ IGHD6-13_star_01_11: 0.0075740010820001535
173
+ IGHD6-13_star_01_12: 0.006492000927428702
174
+ IGHD6-13_star_01_13: 0.005410000772857251
175
+ IGHD6-13_star_01_14: 0.0043280006182858
176
+ IGHD6-13_star_01_15: 0.0032460004637143497
177
+ IGHD6-13_star_01_16: 0.0021640003091428993
178
+ IGHD6-13_star_01_17: 0.001082000154571449
179
+ IGHD6-13_star_01_18: 0.009738001391143055
180
+ IGHD6-13_star_01_19: 0.009738001391143055
181
+ IGHD6-13_star_01_2: 0.009738001391143055
182
+ IGHD6-13_star_01_20: 0.009738001391143055
183
+ IGHD6-13_star_01_3: 0.01947600278228611
184
+ IGHD6-13_star_01_4: 0.01947600278228611
185
+ IGHD6-13_star_01_5: 0.009738001391143055
186
+ IGHD6-13_star_01_6: 0.009738001391143055
187
+ IGHD6-13_star_01_7: 0.009738001391143055
188
+ IGHD6-13_star_01_8: 0.009738001391143055
189
+ IGHD6-13_star_01_9: 0.009738001391143055
190
+ insert_left_A: 0.15319134841509058
191
+ insert_left_C: 0.2757444271471631
192
+ insert_left_G: 0.18995727203471233
193
+ insert_left_T: 0.19608492597131594
194
+ - !!python/object:python.hmmwriter.State
195
+ emissions:
196
+ probs:
197
+ A: 0.042073957702351575
198
+ C: 0.042073957702351575
199
+ G: 0.8737781268929452
200
+ T: 0.042073957702351575
201
+ track: nukes
202
+ extras:
203
+ ambiguous_char: N
204
+ ambiguous_emission_prob: 0.25
205
+ germline: G
206
+ name: IGHD6-13_star_01_0
207
+ transitions:
208
+ IGHD6-13_star_01_1: 0.9615384615384616
209
+ end: 0.03846153846153846
210
+ - !!python/object:python.hmmwriter.State
211
+ emissions:
212
+ probs:
213
+ A: 0.04162444753266621
214
+ C: 0.04162444753266621
215
+ G: 0.8751266574020014
216
+ T: 0.04162444753266621
217
+ track: nukes
218
+ extras:
219
+ ambiguous_char: N
220
+ ambiguous_emission_prob: 0.25
221
+ germline: G
222
+ name: IGHD6-13_star_01_1
223
+ transitions:
224
+ IGHD6-13_star_01_2: 0.9615384615384616
225
+ end: 0.03846153846153846
226
+ - !!python/object:python.hmmwriter.State
227
+ emissions:
228
+ probs:
229
+ A: 0.04135603063103641
230
+ C: 0.04135603063103641
231
+ G: 0.8759319081068908
232
+ T: 0.04135603063103641
233
+ track: nukes
234
+ extras:
235
+ ambiguous_char: N
236
+ ambiguous_emission_prob: 0.25
237
+ germline: G
238
+ name: IGHD6-13_star_01_2
239
+ transitions:
240
+ IGHD6-13_star_01_3: 0.9615384615384616
241
+ end: 0.03846153846153846
242
+ - !!python/object:python.hmmwriter.State
243
+ emissions:
244
+ probs:
245
+ A: 0.04086099298426217
246
+ C: 0.04086099298426217
247
+ G: 0.04086099298426217
248
+ T: 0.8774170210472135
249
+ track: nukes
250
+ extras:
251
+ ambiguous_char: N
252
+ ambiguous_emission_prob: 0.25
253
+ germline: T
254
+ name: IGHD6-13_star_01_3
255
+ transitions:
256
+ IGHD6-13_star_01_4: 0.9615384615384616
257
+ end: 0.03846153846153846
258
+ - !!python/object:python.hmmwriter.State
259
+ emissions:
260
+ probs:
261
+ A: 0.8808780506152474
262
+ C: 0.039707316461584215
263
+ G: 0.039707316461584215
264
+ T: 0.039707316461584215
265
+ track: nukes
266
+ extras:
267
+ ambiguous_char: N
268
+ ambiguous_emission_prob: 0.25
269
+ germline: A
270
+ name: IGHD6-13_star_01_4
271
+ transitions:
272
+ IGHD6-13_star_01_5: 0.9615384615384616
273
+ end: 0.03846153846153846
274
+ - !!python/object:python.hmmwriter.State
275
+ emissions:
276
+ probs:
277
+ A: 0.04832916638623033
278
+ C: 0.04832916638623033
279
+ G: 0.04832916638623033
280
+ T: 0.855012500841309
281
+ track: nukes
282
+ extras:
283
+ ambiguous_char: N
284
+ ambiguous_emission_prob: 0.25
285
+ germline: T
286
+ name: IGHD6-13_star_01_5
287
+ transitions:
288
+ IGHD6-13_star_01_6: 0.9615384615384616
289
+ end: 0.03846153846153846
290
+ - !!python/object:python.hmmwriter.State
291
+ emissions:
292
+ probs:
293
+ A: 0.8512593756309818
294
+ C: 0.04958020812300608
295
+ G: 0.04958020812300608
296
+ T: 0.04958020812300608
297
+ track: nukes
298
+ extras:
299
+ ambiguous_char: N
300
+ ambiguous_emission_prob: 0.25
301
+ germline: A
302
+ name: IGHD6-13_star_01_6
303
+ transitions:
304
+ IGHD6-13_star_01_7: 1.0
305
+ - !!python/object:python.hmmwriter.State
306
+ emissions:
307
+ probs:
308
+ A: 0.11016291641427396
309
+ C: 0.03672097213809133
310
+ G: 0.8163951393095434
311
+ T: 0.03672097213809133
312
+ track: nukes
313
+ extras:
314
+ ambiguous_char: N
315
+ ambiguous_emission_prob: 0.25
316
+ germline: G
317
+ name: IGHD6-13_star_01_7
318
+ transitions:
319
+ IGHD6-13_star_01_8: 0.989010989010989
320
+ end: 0.010989010989011004
321
+ - !!python/object:python.hmmwriter.State
322
+ emissions:
323
+ probs:
324
+ A: 0.03578599530026128
325
+ C: 0.8926420140992162
326
+ G: 0.03578599530026128
327
+ T: 0.03578599530026128
328
+ track: nukes
329
+ extras:
330
+ ambiguous_char: N
331
+ ambiguous_emission_prob: 0.25
332
+ germline: C
333
+ name: IGHD6-13_star_01_8
334
+ transitions:
335
+ IGHD6-13_star_01_9: 0.978021978021978
336
+ end: 0.02197802197802199
337
+ - !!python/object:python.hmmwriter.State
338
+ emissions:
339
+ probs:
340
+ A: 0.90041115338425
341
+ C: 0.03319628220525
342
+ G: 0.03319628220525
343
+ T: 0.03319628220525
344
+ track: nukes
345
+ extras:
346
+ ambiguous_char: N
347
+ ambiguous_emission_prob: 0.25
348
+ germline: A
349
+ name: IGHD6-13_star_01_9
350
+ transitions:
351
+ IGHD6-13_star_01_10: 0.967032967032967
352
+ end: 0.032967032967032975
353
+ - !!python/object:python.hmmwriter.State
354
+ emissions:
355
+ probs:
356
+ A: 0.03333333333333333
357
+ C: 0.03333333333333333
358
+ G: 0.9
359
+ T: 0.03333333333333333
360
+ track: nukes
361
+ extras:
362
+ ambiguous_char: N
363
+ ambiguous_emission_prob: 0.25
364
+ germline: G
365
+ name: IGHD6-13_star_01_10
366
+ transitions:
367
+ IGHD6-13_star_01_11: 0.956043956043956
368
+ end: 0.043956043956043966
369
+ - !!python/object:python.hmmwriter.State
370
+ emissions:
371
+ probs:
372
+ A: 0.03333333333333333
373
+ C: 0.9
374
+ G: 0.03333333333333333
375
+ T: 0.03333333333333333
376
+ track: nukes
377
+ extras:
378
+ ambiguous_char: N
379
+ ambiguous_emission_prob: 0.25
380
+ germline: C
381
+ name: IGHD6-13_star_01_11
382
+ transitions:
383
+ IGHD6-13_star_01_12: 0.945054945054945
384
+ end: 0.054945054945054944
385
+ - !!python/object:python.hmmwriter.State
386
+ emissions:
387
+ probs:
388
+ A: 0.8970864585436605
389
+ C: 0.0343045138187798
390
+ G: 0.0343045138187798
391
+ T: 0.0343045138187798
392
+ track: nukes
393
+ extras:
394
+ ambiguous_char: N
395
+ ambiguous_emission_prob: 0.25
396
+ germline: A
397
+ name: IGHD6-13_star_01_12
398
+ transitions:
399
+ IGHD6-13_star_01_13: 0.9340659340659341
400
+ end: 0.06593406593406594
401
+ - !!python/object:python.hmmwriter.State
402
+ emissions:
403
+ probs:
404
+ A: 0.045901215172614154
405
+ C: 0.09180243034522831
406
+ G: 0.8163951393095434
407
+ T: 0.045901215172614154
408
+ track: nukes
409
+ extras:
410
+ ambiguous_char: N
411
+ ambiguous_emission_prob: 0.25
412
+ germline: G
413
+ name: IGHD6-13_star_01_13
414
+ transitions:
415
+ IGHD6-13_star_01_14: 0.9230769230769231
416
+ end: 0.07692307692307691
417
+ - !!python/object:python.hmmwriter.State
418
+ emissions:
419
+ probs:
420
+ A: 0.03779855045065052
421
+ C: 0.8866043486480484
422
+ G: 0.03779855045065052
423
+ T: 0.03779855045065052
424
+ track: nukes
425
+ extras:
426
+ ambiguous_char: N
427
+ ambiguous_emission_prob: 0.25
428
+ germline: C
429
+ name: IGHD6-13_star_01_14
430
+ transitions:
431
+ IGHD6-13_star_01_15: 0.8846153846153846
432
+ end: 0.11538461538461536
433
+ - !!python/object:python.hmmwriter.State
434
+ emissions:
435
+ probs:
436
+ A: 0.04184768490474884
437
+ C: 0.04184768490474884
438
+ G: 0.04184768490474884
439
+ T: 0.8744569452857535
440
+ track: nukes
441
+ extras:
442
+ ambiguous_char: N
443
+ ambiguous_emission_prob: 0.25
444
+ germline: T
445
+ name: IGHD6-13_star_01_15
446
+ transitions:
447
+ IGHD6-13_star_01_16: 0.9102564102564102
448
+ end: 0.08974358974358974
449
+ - !!python/object:python.hmmwriter.State
450
+ emissions:
451
+ probs:
452
+ A: 0.04045667141156569
453
+ C: 0.04045667141156569
454
+ G: 0.8786299857653029
455
+ T: 0.04045667141156569
456
+ track: nukes
457
+ extras:
458
+ ambiguous_char: N
459
+ ambiguous_emission_prob: 0.25
460
+ germline: G
461
+ name: IGHD6-13_star_01_16
462
+ transitions:
463
+ IGHD6-13_star_01_17: 0.9358974358974359
464
+ end: 0.0641025641025641
465
+ - !!python/object:python.hmmwriter.State
466
+ emissions:
467
+ probs:
468
+ A: 0.04193819402378993
469
+ C: 0.04193819402378993
470
+ G: 0.8741854179286301
471
+ T: 0.04193819402378993
472
+ track: nukes
473
+ extras:
474
+ ambiguous_char: N
475
+ ambiguous_emission_prob: 0.25
476
+ germline: G
477
+ name: IGHD6-13_star_01_17
478
+ transitions:
479
+ IGHD6-13_star_01_18: 0.9615384615384616
480
+ end: 0.03846153846153846
481
+ - !!python/object:python.hmmwriter.State
482
+ emissions:
483
+ probs:
484
+ A: 0.04235381895368085
485
+ C: 0.04235381895368085
486
+ G: 0.04235381895368085
487
+ T: 0.8729385431389575
488
+ track: nukes
489
+ extras:
490
+ ambiguous_char: N
491
+ ambiguous_emission_prob: 0.25
492
+ germline: T
493
+ name: IGHD6-13_star_01_18
494
+ transitions:
495
+ IGHD6-13_star_01_19: 0.9615384615384616
496
+ end: 0.03846153846153846
497
+ - !!python/object:python.hmmwriter.State
498
+ emissions:
499
+ probs:
500
+ A: 0.8728027794603958
501
+ C: 0.04239907351320141
502
+ G: 0.04239907351320141
503
+ T: 0.04239907351320141
504
+ track: nukes
505
+ extras:
506
+ ambiguous_char: N
507
+ ambiguous_emission_prob: 0.25
508
+ germline: A
509
+ name: IGHD6-13_star_01_19
510
+ transitions:
511
+ IGHD6-13_star_01_20: 0.9615384615384616
512
+ end: 0.03846153846153846
513
+ - !!python/object:python.hmmwriter.State
514
+ emissions:
515
+ probs:
516
+ A: 0.042073957702351575
517
+ C: 0.8737781268929452
518
+ G: 0.042073957702351575
519
+ T: 0.042073957702351575
520
+ track: nukes
521
+ extras:
522
+ ambiguous_char: N
523
+ ambiguous_emission_prob: 0.25
524
+ germline: C
525
+ name: IGHD6-13_star_01_20
526
+ transitions:
527
+ end: 1.0
528
+ tracks:
529
+ nukes:
530
+ - A
531
+ - C
532
+ - G
533
+ - T