partis-bcr 1.0.5__py3-none-any.whl → 1.0.7__py3-none-any.whl

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Files changed (139) hide show
  1. bin/partis-test.py +4 -1
  2. packages/ham/bcrham +0 -0
  3. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/partis-test.py +4 -1
  4. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/METADATA +2 -1
  5. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/RECORD +98 -139
  6. python/utils.py +1 -1
  7. test/new-results/test/parameters/simu/hmm/all-mean-mute-freqs.csv +3 -3
  8. test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv +11 -11
  9. test/new-results/test/parameters/simu/hmm/all-probs.csv +3 -13
  10. test/new-results/test/parameters/simu/hmm/cluster_size.csv +1 -1
  11. test/new-results/test/parameters/simu/hmm/d-mean-mute-freqs.csv +6 -6
  12. test/new-results/test/parameters/simu/hmm/d-mean-n-muted.csv +3 -3
  13. test/new-results/test/parameters/simu/hmm/d_gene-d_3p_del-probs.csv +1 -6
  14. test/new-results/test/parameters/simu/hmm/d_gene-d_5p_del-probs.csv +2 -9
  15. test/new-results/test/parameters/simu/hmm/d_gene-probs.csv +1 -5
  16. test/new-results/test/parameters/simu/hmm/d_gene-vd_insertion-probs.csv +2 -10
  17. test/new-results/test/parameters/simu/hmm/dj_insertion_content.csv +4 -4
  18. test/new-results/test/parameters/simu/hmm/fv_insertion-probs.csv +2 -3
  19. test/new-results/test/parameters/simu/hmm/germline-sets/igh/extras.csv +0 -6
  20. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighd.fasta +0 -8
  21. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighj.fasta +0 -2
  22. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighv.fasta +0 -10
  23. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-13_star_01.yaml +268 -267
  24. test/new-results/test/parameters/simu/hmm/hmms/IGHJ4_star_02.yaml +306 -306
  25. test/new-results/test/parameters/simu/hmm/hmms/IGHJ6_star_02.yaml +284 -284
  26. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-66_star_02.yaml +1191 -1191
  27. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-7_star_05.yaml +2 -2
  28. test/new-results/test/parameters/simu/hmm/j-mean-mute-freqs.csv +5 -5
  29. test/new-results/test/parameters/simu/hmm/j-mean-n-muted.csv +4 -4
  30. test/new-results/test/parameters/simu/hmm/j_gene-dj_insertion-probs.csv +2 -9
  31. test/new-results/test/parameters/simu/hmm/j_gene-j_3p_del-probs.csv +1 -2
  32. test/new-results/test/parameters/simu/hmm/j_gene-j_5p_del-probs.csv +2 -7
  33. test/new-results/test/parameters/simu/hmm/j_gene-probs.csv +1 -2
  34. test/new-results/test/parameters/simu/hmm/jf_insertion-probs.csv +1 -1
  35. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-13_star_01.csv +13 -16
  36. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ4_star_02.csv +40 -44
  37. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ6_star_02.csv +0 -2
  38. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-66_star_02.csv +291 -293
  39. test/new-results/test/parameters/simu/hmm/seq_content.csv +4 -4
  40. test/new-results/test/parameters/simu/hmm/v-mean-mute-freqs.csv +3 -3
  41. test/new-results/test/parameters/simu/hmm/v-mean-n-muted.csv +7 -7
  42. test/new-results/test/parameters/simu/hmm/v_gene-probs.csv +1 -6
  43. test/new-results/test/parameters/simu/hmm/v_gene-v_3p_del-probs.csv +1 -7
  44. test/new-results/test/parameters/simu/hmm/v_gene-v_5p_del-probs.csv +1 -6
  45. test/new-results/test/parameters/simu/hmm/vd_insertion_content.csv +4 -4
  46. test/new-results/test/parameters/simu/sw/all-mean-mute-freqs.csv +3 -3
  47. test/new-results/test/parameters/simu/sw/all-mean-n-muted.csv +8 -8
  48. test/new-results/test/parameters/simu/sw/all-probs.csv +1 -9
  49. test/new-results/test/parameters/simu/sw/cluster_size.csv +1 -1
  50. test/new-results/test/parameters/simu/sw/d-mean-mute-freqs.csv +5 -5
  51. test/new-results/test/parameters/simu/sw/d-mean-n-muted.csv +3 -3
  52. test/new-results/test/parameters/simu/sw/d_gene-d_3p_del-probs.csv +1 -7
  53. test/new-results/test/parameters/simu/sw/d_gene-d_5p_del-probs.csv +1 -7
  54. test/new-results/test/parameters/simu/sw/d_gene-probs.csv +1 -5
  55. test/new-results/test/parameters/simu/sw/d_gene-vd_insertion-probs.csv +1 -8
  56. test/new-results/test/parameters/simu/sw/dj_insertion_content.csv +4 -4
  57. test/new-results/test/parameters/simu/sw/fv_insertion-probs.csv +1 -1
  58. test/new-results/test/parameters/simu/sw/germline-sets/igh/extras.csv +0 -6
  59. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighd.fasta +0 -8
  60. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighj.fasta +0 -2
  61. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighv.fasta +0 -10
  62. test/new-results/test/parameters/simu/sw/hmms/IGHD6-13_star_01.yaml +268 -267
  63. test/new-results/test/parameters/simu/sw/hmms/IGHJ4_star_02.yaml +306 -306
  64. test/new-results/test/parameters/simu/sw/hmms/IGHJ6_star_02.yaml +22 -22
  65. test/new-results/test/parameters/simu/sw/hmms/IGHV3-66_star_02.yaml +1191 -1191
  66. test/new-results/test/parameters/simu/sw/hmms/IGHV3-7_star_05.yaml +2 -2
  67. test/new-results/test/parameters/simu/sw/j-mean-mute-freqs.csv +4 -4
  68. test/new-results/test/parameters/simu/sw/j-mean-n-muted.csv +3 -3
  69. test/new-results/test/parameters/simu/sw/j_gene-dj_insertion-probs.csv +1 -7
  70. test/new-results/test/parameters/simu/sw/j_gene-j_3p_del-probs.csv +1 -2
  71. test/new-results/test/parameters/simu/sw/j_gene-j_5p_del-probs.csv +1 -7
  72. test/new-results/test/parameters/simu/sw/j_gene-probs.csv +1 -2
  73. test/new-results/test/parameters/simu/sw/jf_insertion-probs.csv +1 -1
  74. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-13_star_01.csv +13 -16
  75. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ4_star_02.csv +40 -48
  76. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv +291 -293
  77. test/new-results/test/parameters/simu/sw/seq_content.csv +4 -4
  78. test/new-results/test/parameters/simu/sw/v-mean-mute-freqs.csv +3 -3
  79. test/new-results/test/parameters/simu/sw/v-mean-n-muted.csv +7 -7
  80. test/new-results/test/parameters/simu/sw/v_gene-probs.csv +1 -6
  81. test/new-results/test/parameters/simu/sw/v_gene-v_3p_del-probs.csv +1 -7
  82. test/new-results/test/parameters/simu/sw/v_gene-v_5p_del-probs.csv +1 -6
  83. test/new-results/test/parameters/simu/sw/vd_insertion_content.csv +4 -4
  84. test/new-results/test/parameters/simu/sw-cache.yaml +1 -1
  85. test/new-results/test.log +24 -258
  86. test/test.py +4 -1
  87. bin/partis-pip +0 -116
  88. test/new-results/test/parameters/simu/hmm/hmms/IGHD1-20_star_01.yaml +0 -449
  89. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-16_star_02.yaml +0 -870
  90. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-22_star_01.yaml +0 -744
  91. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-19_star_01.yaml +0 -534
  92. test/new-results/test/parameters/simu/hmm/hmms/IGHJ1_star_01.yaml +0 -986
  93. test/new-results/test/parameters/simu/hmm/hmms/IGHV1-18_star_01.yaml +0 -4484
  94. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-23_star_01.yaml +0 -4484
  95. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-4_star_09.yaml +0 -4438
  96. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-61_star_01.yaml +0 -4529
  97. test/new-results/test/parameters/simu/hmm/hmms/IGHV5-51_star_01.yaml +0 -4484
  98. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD1-20_star_01.csv +0 -9
  99. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-16_star_02.csv +0 -30
  100. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-22_star_01.csv +0 -32
  101. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-19_star_01.csv +0 -22
  102. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ1_star_01.csv +0 -50
  103. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV1-18_star_01.csv +0 -297
  104. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-23_star_01.csv +0 -297
  105. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-4_star_09.csv +0 -291
  106. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-61_star_01.csv +0 -300
  107. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV5-51_star_01.csv +0 -296
  108. test/new-results/test/parameters/simu/sw/hmms/IGHD1-20_star_01.yaml +0 -449
  109. test/new-results/test/parameters/simu/sw/hmms/IGHD3-16_star_02.yaml +0 -870
  110. test/new-results/test/parameters/simu/sw/hmms/IGHD3-22_star_01.yaml +0 -744
  111. test/new-results/test/parameters/simu/sw/hmms/IGHD6-19_star_01.yaml +0 -534
  112. test/new-results/test/parameters/simu/sw/hmms/IGHJ1_star_01.yaml +0 -986
  113. test/new-results/test/parameters/simu/sw/hmms/IGHV1-18_star_01.yaml +0 -4484
  114. test/new-results/test/parameters/simu/sw/hmms/IGHV3-23_star_01.yaml +0 -4484
  115. test/new-results/test/parameters/simu/sw/hmms/IGHV4-4_star_09.yaml +0 -4438
  116. test/new-results/test/parameters/simu/sw/hmms/IGHV4-61_star_01.yaml +0 -4529
  117. test/new-results/test/parameters/simu/sw/hmms/IGHV5-51_star_01.yaml +0 -4484
  118. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD1-20_star_01.csv +0 -9
  119. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-16_star_02.csv +0 -30
  120. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-22_star_01.csv +0 -32
  121. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-19_star_01.csv +0 -20
  122. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ1_star_01.csv +0 -50
  123. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV1-18_star_01.csv +0 -297
  124. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-23_star_01.csv +0 -297
  125. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-4_star_09.csv +0 -291
  126. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-61_star_01.csv +0 -300
  127. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV5-51_star_01.csv +0 -296
  128. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/cf-alleles.py +0 -0
  129. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/cf-germlines.py +0 -0
  130. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/compare-plotdirs.py +0 -0
  131. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/extract-pairing-info.py +0 -0
  132. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/gctree-run.py +0 -0
  133. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/get-naive-probabilities.py +0 -0
  134. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/parse-output.py +0 -0
  135. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/split-loci.py +0 -0
  136. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/WHEEL +0 -0
  137. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/entry_points.txt +0 -0
  138. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/licenses/COPYING +0 -0
  139. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/hmm/seq_content.csv CHANGED
@@ -1,5 +1,5 @@
1
1
  seq_content,count
2
- A,2932
3
- C,3445
4
- G,3948
5
- T,2762
2
+ A,807
3
+ C,886
4
+ G,1111
5
+ T,755
test/new-results/test/parameters/simu/hmm/v-mean-mute-freqs.csv CHANGED
@@ -1,8 +1,8 @@
1
1
  bin_low_edge,contents,binlabel,error
2
2
  -0.01,0.0,,0.0
3
- 0.0,0.4166666666666667,,0.10758287072798381
4
- 0.01,0.4722222222222222,,0.1145307118227128
5
- 0.02,0.1111111111111111,,0.05555555555555555
3
+ 0.0,0.0,,0.0
4
+ 0.01,0.7,,0.2645751311064591
5
+ 0.02,0.3,,0.17320508075688773
6
6
  0.03,0.0,,0.0
7
7
  0.04,0.0,,0.0
8
8
  0.05,0.0,,0.0
test/new-results/test/parameters/simu/hmm/v-mean-n-muted.csv CHANGED
@@ -1,12 +1,12 @@
1
1
  bin_low_edge,contents,binlabel,error
2
2
  -1.5,0.0,,0.0
3
- -0.5,10.0,,3.1622776601683795
4
- 0.5,3.0,,1.7320508075688772
5
- 1.5,2.0,,1.4142135623730951
6
- 2.5,7.0,,2.6457513110645907
7
- 3.5,7.0,,2.6457513110645907
8
- 4.5,3.0,,1.7320508075688772
9
- 5.5,3.0,,1.7320508075688772
3
+ -0.5,0.0,,0.0
4
+ 0.5,0.0,,0.0
5
+ 1.5,0.0,,0.0
6
+ 2.5,2.0,,1.4142135623730951
7
+ 3.5,4.0,,2.0
8
+ 4.5,1.0,,1.0
9
+ 5.5,2.0,,1.4142135623730951
10
10
  6.5,1.0,,1.0
11
11
  7.5,0.0,,0.0
12
12
  8.5,0.0,,0.0
test/new-results/test/parameters/simu/hmm/v_gene-probs.csv CHANGED
@@ -1,8 +1,3 @@
1
1
  v_gene,count
2
2
  IGHV3-7*05,3
3
- IGHV3-66*02,14
4
- IGHV3-23*01,2
5
- IGHV4-4*09,1
6
- IGHV4-61*01,8
7
- IGHV1-18*01,7
8
- IGHV5-51*01,1
3
+ IGHV3-66*02,7
test/new-results/test/parameters/simu/hmm/v_gene-v_3p_del-probs.csv CHANGED
@@ -1,9 +1,3 @@
1
1
  v_3p_del,v_gene,count
2
2
  0,IGHV3-7*05,3
3
- 2,IGHV3-66*02,13
4
- 0,IGHV3-23*01,2
5
- 3,IGHV4-4*09,1
6
- 0,IGHV4-61*01,8
7
- 0,IGHV1-18*01,7
8
- 1,IGHV5-51*01,1
9
- 0,IGHV3-66*02,1
3
+ 2,IGHV3-66*02,7
test/new-results/test/parameters/simu/hmm/v_gene-v_5p_del-probs.csv CHANGED
@@ -1,8 +1,3 @@
1
1
  v_5p_del,v_gene,count
2
2
  0,IGHV3-7*05,3
3
- 0,IGHV3-66*02,14
4
- 0,IGHV3-23*01,2
5
- 0,IGHV4-4*09,1
6
- 0,IGHV4-61*01,8
7
- 0,IGHV1-18*01,7
8
- 0,IGHV5-51*01,1
3
+ 0,IGHV3-66*02,7
test/new-results/test/parameters/simu/hmm/vd_insertion_content.csv CHANGED
@@ -1,5 +1,5 @@
1
1
  vd_insertion_content,count
2
- A,16
3
- C,64
4
- G,23
5
- T,38
2
+ A,0
3
+ C,14
4
+ G,3
5
+ T,10
test/new-results/test/parameters/simu/sw/all-mean-mute-freqs.csv CHANGED
@@ -1,8 +1,8 @@
1
1
  bin_low_edge,contents,binlabel,error
2
2
  -0.01,0.0,,0.0
3
- 0.0,0.3888888888888889,,0.10393492741038726
4
- 0.01,0.5,,0.1178511301977579
5
- 0.02,0.1111111111111111,,0.05555555555555555
3
+ 0.0,0.0,,0.0
4
+ 0.01,0.6,,0.2449489742783178
5
+ 0.02,0.4,,0.2
6
6
  0.03,0.0,,0.0
7
7
  0.04,0.0,,0.0
8
8
  0.05,0.0,,0.0
test/new-results/test/parameters/simu/sw/all-mean-n-muted.csv CHANGED
@@ -1,13 +1,13 @@
1
1
  bin_low_edge,contents,binlabel,error
2
2
  -1.5,0.0,,0.0
3
- -0.5,9.0,,3.0
4
- 0.5,3.0,,1.7320508075688772
5
- 1.5,1.0,,1.0
6
- 2.5,1.0,,1.0
7
- 3.5,6.0,,2.449489742783178
8
- 4.5,5.0,,2.23606797749979
9
- 5.5,6.0,,2.449489742783178
10
- 6.5,3.0,,1.7320508075688772
3
+ -0.5,0.0,,0.0
4
+ 0.5,0.0,,0.0
5
+ 1.5,0.0,,0.0
6
+ 2.5,0.0,,0.0
7
+ 3.5,3.0,,1.7320508075688772
8
+ 4.5,1.0,,1.0
9
+ 5.5,2.0,,1.4142135623730951
10
+ 6.5,2.0,,1.4142135623730951
11
11
  7.5,2.0,,1.4142135623730951
12
12
  8.5,0.0,,0.0
13
13
  9.5,0.0,,0.0
test/new-results/test/parameters/simu/sw/all-probs.csv CHANGED
@@ -1,12 +1,4 @@
1
1
  v_gene,d_gene,j_gene,v_5p_del,v_3p_del,d_5p_del,d_3p_del,j_5p_del,j_3p_del,fv_insertion,vd_insertion,dj_insertion,jf_insertion,cdr3_length,count
2
2
  IGHV3-7*05,IGHD6-13*01,IGHJ6*02,0,0,9,0,17,0,0,6,19,0,63,3
3
- IGHV3-66*02,IGHD6-13*01,IGHJ4*02,0,2,3,6,8,0,0,2,1,0,33,10
3
+ IGHV3-66*02,IGHD6-13*01,IGHJ4*02,0,2,3,6,8,0,0,2,1,0,33,6
4
4
  IGHV3-66*02,IGHD6-13*01,IGHJ4*02,0,2,4,6,8,0,0,3,1,0,33,1
5
- IGHV4-4*09,IGHD6-13*01,IGHJ4*02,0,3,0,7,7,0,0,10,6,0,48,1
6
- IGHV1-18*01,IGHD6-13*01,IGHJ4*02,0,0,2,5,5,0,0,9,5,0,51,7
7
- IGHV3-23*01,IGHD3-16*02,IGHJ4*02,0,0,8,0,4,0,0,0,1,0,54,2
8
- IGHV4-61*01,IGHD3-22*01,IGHJ1*01,0,0,0,0,3,0,0,0,0,0,60,7
9
- IGHV4-61*01,IGHD3-22*01,IGHJ1*01,0,0,0,0,9,0,0,0,10,0,64,1
10
- IGHV3-66*02,IGHD1-20*01,IGHJ4*02,0,2,3,6,8,0,0,6,7,0,39,2
11
- IGHV5-51*01,IGHD6-19*01,IGHJ4*02,0,1,0,2,0,0,0,2,0,0,48,1
12
- IGHV3-66*02,IGHD6-13*01,IGHJ4*02,0,0,2,7,7,0,0,17,7,0,57,1
test/new-results/test/parameters/simu/sw/cluster_size.csv CHANGED
@@ -1,2 +1,2 @@
1
1
  cluster_size,count
2
- 1,36
2
+ 1,10
test/new-results/test/parameters/simu/sw/d-mean-mute-freqs.csv CHANGED
@@ -1,14 +1,14 @@
1
1
  bin_low_edge,contents,binlabel,error
2
2
  -0.01,0.0,,0.0
3
- 0.0,0.7222222222222222,,0.14163943093313291
3
+ 0.0,0.9,,0.3
4
4
  0.01,0.0,,0.0
5
5
  0.02,0.0,,0.0
6
- 0.03,0.16666666666666666,,0.06804138174397717
6
+ 0.03,0.0,,0.0
7
7
  0.04,0.0,,0.0
8
8
  0.05,0.0,,0.0
9
- 0.06,0.05555555555555555,,0.03928371006591931
10
- 0.07,0.027777777777777776,,0.027777777777777776
11
- 0.08,0.027777777777777776,,0.027777777777777776
9
+ 0.06,0.0,,0.0
10
+ 0.07,0.0,,0.0
11
+ 0.08,0.1,,0.1
12
12
  0.09,0.0,,0.0
13
13
  0.1,0.0,,0.0
14
14
  0.11,0.0,,0.0
test/new-results/test/parameters/simu/sw/d-mean-n-muted.csv CHANGED
@@ -1,8 +1,8 @@
1
1
  bin_low_edge,contents,binlabel,error
2
2
  -1.5,0.0,,0.0
3
- -0.5,26.0,,5.0990195135927845
4
- 0.5,8.0,,2.8284271247461903
5
- 1.5,2.0,,1.4142135623730951
3
+ -0.5,9.0,,3.0
4
+ 0.5,1.0,,1.0
5
+ 1.5,0.0,,0.0
6
6
  2.5,0.0,,0.0
7
7
  3.5,0.0,,0.0
8
8
  4.5,0.0,,0.0
test/new-results/test/parameters/simu/sw/d_gene-d_3p_del-probs.csv CHANGED
@@ -1,9 +1,3 @@
1
1
  d_3p_del,d_gene,count
2
2
  0,IGHD6-13*01,3
3
- 6,IGHD6-13*01,11
4
- 7,IGHD6-13*01,2
5
- 5,IGHD6-13*01,7
6
- 0,IGHD3-16*02,2
7
- 0,IGHD3-22*01,8
8
- 6,IGHD1-20*01,2
9
- 2,IGHD6-19*01,1
3
+ 6,IGHD6-13*01,7
test/new-results/test/parameters/simu/sw/d_gene-d_5p_del-probs.csv CHANGED
@@ -1,10 +1,4 @@
1
1
  d_5p_del,d_gene,count
2
2
  9,IGHD6-13*01,3
3
- 3,IGHD6-13*01,10
3
+ 3,IGHD6-13*01,6
4
4
  4,IGHD6-13*01,1
5
- 0,IGHD6-13*01,1
6
- 2,IGHD6-13*01,8
7
- 8,IGHD3-16*02,2
8
- 0,IGHD3-22*01,8
9
- 3,IGHD1-20*01,2
10
- 0,IGHD6-19*01,1
test/new-results/test/parameters/simu/sw/d_gene-probs.csv CHANGED
@@ -1,6 +1,2 @@
1
1
  d_gene,count
2
- IGHD6-13*01,23
3
- IGHD3-16*02,2
4
- IGHD3-22*01,8
5
- IGHD1-20*01,2
6
- IGHD6-19*01,1
2
+ IGHD6-13*01,10
test/new-results/test/parameters/simu/sw/d_gene-vd_insertion-probs.csv CHANGED
@@ -1,11 +1,4 @@
1
1
  vd_insertion,d_gene,count
2
2
  6,IGHD6-13*01,3
3
- 2,IGHD6-13*01,10
3
+ 2,IGHD6-13*01,6
4
4
  3,IGHD6-13*01,1
5
- 10,IGHD6-13*01,1
6
- 9,IGHD6-13*01,7
7
- 0,IGHD3-16*02,2
8
- 0,IGHD3-22*01,8
9
- 6,IGHD1-20*01,2
10
- 2,IGHD6-19*01,1
11
- 17,IGHD6-13*01,1
test/new-results/test/parameters/simu/sw/dj_insertion_content.csv CHANGED
@@ -1,5 +1,5 @@
1
1
  dj_insertion_content,count
2
- A,20
3
- C,57
4
- G,23
5
- T,42
2
+ A,11
3
+ C,16
4
+ G,16
5
+ T,21
test/new-results/test/parameters/simu/sw/fv_insertion-probs.csv CHANGED
@@ -1,2 +1,2 @@
1
1
  fv_insertion,count
2
- 0,36
2
+ 0,10
test/new-results/test/parameters/simu/sw/germline-sets/igh/extras.csv CHANGED
@@ -1,11 +1,5 @@
1
1
  gene,cyst_position,tryp_position,phen_position,aligned_seq
2
- IGHV1-18*01,285,,,
3
2
  IGHV3-7*05,285,,,
4
- IGHV5-51*01,285,,,
5
3
  IGHV3-66*02,282,,,
6
- IGHV3-23*01,285,,,
7
- IGHV4-61*01,288,,,
8
- IGHV4-4*09,282,,,
9
4
  IGHJ4*02,,14,,
10
5
  IGHJ6*02,,29,,
11
- IGHJ1*01,,18,,
test/new-results/test/parameters/simu/sw/germline-sets/igh/ighd.fasta CHANGED
@@ -1,10 +1,2 @@
1
- >IGHD1-20*01
2
- GGTATAACTGGAACGAC
3
- >IGHD3-16*02
4
- GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC
5
- >IGHD3-22*01
6
- GTATTACTATGATAGTAGTGGTTATTACTAC
7
1
  >IGHD6-13*01
8
2
  GGGTATAGCAGCAGCTGGTAC
9
- >IGHD6-19*01
10
- GGGTATAGCAGTGGCTGGTAC
test/new-results/test/parameters/simu/sw/germline-sets/igh/ighj.fasta CHANGED
@@ -1,5 +1,3 @@
1
- >IGHJ1*01
2
- GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
3
1
  >IGHJ4*02
4
2
  ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
5
3
  >IGHJ6*02
test/new-results/test/parameters/simu/sw/germline-sets/igh/ighv.fasta CHANGED
@@ -1,14 +1,4 @@
1
- >IGHV1-18*01
2
- CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA
3
- >IGHV3-23*01
4
- GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA
5
1
  >IGHV3-66*02
6
2
  GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA
7
3
  >IGHV3-7*05
8
4
  GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA
9
- >IGHV4-4*09
10
- CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA
11
- >IGHV4-61*01
12
- CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA
13
- >IGHV5-51*01
14
- GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA