partis-bcr 1.0.11__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl

test/new-results/test/parameters/data/hmm/d_gene-d_5p_del-probs.csv

@@ -0,0 +1,42 @@
+d_5p_del,d_gene,count
+5,IGHD6-13*01,1
+8,IGHD6-13*01,1
+0,IGHD2-8*01,3
+5,IGHD4-17*01,1
+3,IGHD3-3*01,1
+3,IGHD6-13*01,2
+5,IGHD3-10*01,1
+17,IGHD3-16*02,1
+8,IGHD6-6*01,1
+0,IGHD6-13*01,1
+3,IGHD4-4*01,1
+3,IGHD1-20*01,2
+9,IGHD3-10*03,1
+2,IGHD2-15*01,1
+0,IGHD4-4*01,1
+4,IGHD6-13*01,2
+12,IGHD3-10*01,1
+0,IGHD6-6*01,1
+13,IGHD2-15*01,1
+8,IGHD5-5*01,1
+8,IGHD3-16*02,1
+13,IGHD5-5*01,1
+0,IGHD6-19*01,1
+4,IGHD4-17*01,1
+0,IGHD2-21*02,1
+1,IGHD6-13*01,1
+3,IGHD3-16*02,1
+10,IGHD1-26*01,1
+4,IGHD2-15*01,1
+0,IGHD2-15*01,1
+2,IGHD3-10*01,1
+10,IGHD2-8*02,1
+12,IGHD3-22*01,1
+9,IGHD6-13*01,1
+7,IGHD6-6*01,1
+2,IGHD6-6*01,1
+2,IGHD6-13*01,1
+3,IGHD2-15*01,1
+1,IGHD2-21*01,1
+17,IGHD2-2*01,1
+0,IGHD3-22*01,1

test/new-results/test/parameters/data/hmm/d_gene-probs.csv

@@ -0,0 +1,20 @@
+d_gene,count
+IGHD6-13*01,10
+IGHD2-8*01,3
+IGHD4-17*01,2
+IGHD3-3*01,1
+IGHD3-10*01,3
+IGHD3-16*02,3
+IGHD6-6*01,4
+IGHD4-4*01,2
+IGHD1-20*01,2
+IGHD3-10*03,1
+IGHD2-15*01,5
+IGHD5-5*01,2
+IGHD6-19*01,1
+IGHD2-21*02,1
+IGHD1-26*01,1
+IGHD2-8*02,1
+IGHD3-22*01,2
+IGHD2-21*01,1
+IGHD2-2*01,1

test/new-results/test/parameters/data/hmm/d_gene-vd_insertion-probs.csv

@@ -0,0 +1,39 @@
+vd_insertion,d_gene,count
+4,IGHD6-13*01,1
+9,IGHD6-13*01,2
+3,IGHD2-8*01,2
+5,IGHD4-17*01,1
+6,IGHD3-3*01,1
+2,IGHD6-13*01,2
+5,IGHD3-10*01,1
+4,IGHD3-16*02,1
+0,IGHD6-6*01,1
+10,IGHD6-13*01,1
+4,IGHD4-4*01,1
+6,IGHD1-20*01,2
+15,IGHD3-10*03,1
+1,IGHD2-15*01,3
+1,IGHD4-4*01,1
+3,IGHD6-13*01,2
+21,IGHD3-10*01,1
+15,IGHD6-6*01,1
+0,IGHD5-5*01,2
+1,IGHD2-8*01,1
+0,IGHD3-16*02,1
+2,IGHD6-19*01,1
+0,IGHD4-17*01,1
+1,IGHD2-21*02,1
+5,IGHD6-13*01,1
+6,IGHD3-16*02,1
+14,IGHD1-26*01,1
+7,IGHD2-15*01,1
+10,IGHD3-10*01,1
+11,IGHD2-8*02,1
+15,IGHD3-22*01,1
+6,IGHD6-13*01,1
+13,IGHD6-6*01,1
+6,IGHD6-6*01,1
+5,IGHD2-15*01,1
+19,IGHD2-21*01,1
+6,IGHD2-2*01,1
+0,IGHD3-22*01,1

test/new-results/test/parameters/data/hmm/dj_insertion_content.csv

@@ -0,0 +1,5 @@
+dj_insertion_content,count
+A,60
+C,93
+G,69
+T,76

test/new-results/test/parameters/data/hmm/fv_insertion-probs.csv

@@ -0,0 +1,4 @@
+fv_insertion,count
+6,15
+3,27
+0,4

test/new-results/test/parameters/data/hmm/germline-sets/igh/extras.csv

@@ -0,0 +1,23 @@
+gene,cyst_position,tryp_position,phen_position,aligned_seq
+IGHV2-5*02,288,,,
+IGHV4-34*01,282,,,
+IGHV1-2*02,285,,,
+IGHV1-18*01,285,,,
+IGHV3-7*05,285,,,
+IGHV3-69-1*02,282,,,
+IGHV3-11*04,285,,,
+IGHV2-70D*04,288,,,
+IGHV5-51*01,285,,,
+IGHV3-66*02,282,,,
+IGHV4-39*09,288,,,
+IGHV3-9*02,285,,,
+IGHV3-23*01,285,,,
+IGHV4-61*01,288,,,
+IGHV4-4*09,282,,,
+IGHJ4*02,,14,,
+IGHJ2*01,,19,,
+IGHJ3*02,,16,,
+IGHJ6*02,,29,,
+IGHJ5*02,,17,,
+IGHJ1*01,,18,,
+IGHJ6*03,,29,,

test/new-results/test/parameters/data/hmm/germline-sets/igh/ighd.fasta

@@ -0,0 +1,38 @@
+>IGHD1-20*01
+GGTATAACTGGAACGAC
+>IGHD1-26*01
+GGTATAGTGGGAGCTACTAC
+>IGHD2-15*01
+AGGATATTGTAGTGGTGGTAGCTGCTACTCC
+>IGHD2-2*01
+AGGATATTGTAGTAGTACCAGCTGCTATGCC
+>IGHD2-21*01
+AGCATATTGTGGTGGTGATTGCTATTCC
+>IGHD2-21*02
+AGCATATTGTGGTGGTGACTGCTATTCC
+>IGHD2-8*01
+AGGATATTGTACTAATGGTGTATGCTATACC
+>IGHD2-8*02
+AGGATATTGTACTGGTGGTGTATGCTATACC
+>IGHD3-10*01
+GTATTACTATGGTTCGGGGAGTTATTATAAC
+>IGHD3-10*03
+GTATTACTATGGTTCAGGGAGTTATTATAAC
+>IGHD3-16*02
+GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC
+>IGHD3-22*01
+GTATTACTATGATAGTAGTGGTTATTACTAC
+>IGHD3-3*01
+GTATTACGATTTTTGGAGTGGTTATTATACC
+>IGHD4-17*01
+TGACTACGGTGACTAC
+>IGHD4-4*01
+TGACTACAGTAACTAC
+>IGHD5-5*01
+GTGGATACAGCTATGGTTAC
+>IGHD6-13*01
+GGGTATAGCAGCAGCTGGTAC
+>IGHD6-19*01
+GGGTATAGCAGTGGCTGGTAC
+>IGHD6-6*01
+GAGTATAGCAGCTCGTCC

test/new-results/test/parameters/data/hmm/germline-sets/igh/ighj.fasta

@@ -0,0 +1,14 @@
+>IGHJ1*01
+GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>IGHJ2*01
+CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG
+>IGHJ3*02
+TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG
+>IGHJ4*02
+ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>IGHJ5*02
+ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>IGHJ6*02
+ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG
+>IGHJ6*03
+ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG

test/new-results/test/parameters/data/hmm/germline-sets/igh/ighv.fasta

@@ -0,0 +1,30 @@
+>IGHV1-18*01
+CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA
+>IGHV1-2*02
+CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA
+>IGHV2-5*02
+CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC
+>IGHV2-70D*04
+CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC
+>IGHV3-11*04
+CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA
+>IGHV3-23*01
+GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA
+>IGHV3-66*02
+GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA
+>IGHV3-69-1*02
+GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA
+>IGHV3-7*05
+GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA
+>IGHV3-9*02
+GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA
+>IGHV4-34*01
+CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG
+>IGHV4-39*09
+CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA
+>IGHV4-4*09
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA
+>IGHV4-61*01
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA
+>IGHV5-51*01
+GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA

test/new-results/test/parameters/data/hmm/hmms/IGHD1-20_star_01.yaml

@@ -0,0 +1,449 @@
+!!python/object:python.hmmwriter.HMM
+extras:
+  gene_prob: 0.043478260869565216
+  overall_mute_freq: 0.08760869565217394
+  per_gene_mute_freq: 0.10579974645169707
+name: IGHD1-20_star_01
+states:
+- !!python/object:python.hmmwriter.State
+  emissions: null
+  extras: {}
+  name: init
+  transitions:
+    IGHD1-20_star_01_0: 0.0196078431372549
+    IGHD1-20_star_01_1: 0.0196078431372549
+    IGHD1-20_star_01_10: 0.0196078431372549
+    IGHD1-20_star_01_11: 0.0196078431372549
+    IGHD1-20_star_01_12: 0.0196078431372549
+    IGHD1-20_star_01_13: 0.0196078431372549
+    IGHD1-20_star_01_14: 0.0196078431372549
+    IGHD1-20_star_01_15: 0.0196078431372549
+    IGHD1-20_star_01_16: 0.0196078431372549
+    IGHD1-20_star_01_2: 0.0196078431372549
+    IGHD1-20_star_01_3: 0.0392156862745098
+    IGHD1-20_star_01_4: 0.026143790849673207
+    IGHD1-20_star_01_5: 0.013071895424836605
+    IGHD1-20_star_01_6: 4.353815782843751e-18
+    IGHD1-20_star_01_7: 0.0196078431372549
+    IGHD1-20_star_01_8: 0.0196078431372549
+    IGHD1-20_star_01_9: 0.0196078431372549
+    insert_left_A: 0.12531328320802007
+    insert_left_C: 0.2255639097744361
+    insert_left_G: 0.15538847117794488
+    insert_left_T: 0.16040100250626568
+- !!python/object:python.hmmwriter.State
+  emissions:
+    probs:
+      A: 0.8942002535483029
+      C: 0.03526658215056569
+      G: 0.03526658215056569
+      T: 0.03526658215056569
+    track: nukes
+  extras:
+    ambiguous_char: N
+    ambiguous_emission_prob: 0.25
+    germline: A
+  name: insert_left_A
+  transitions:
+    IGHD1-20_star_01_0: 0.014705882352941176
+    IGHD1-20_star_01_1: 0.014705882352941176
+    IGHD1-20_star_01_10: 0.014705882352941176
+    IGHD1-20_star_01_11: 0.014705882352941176
+    IGHD1-20_star_01_12: 0.014705882352941176
+    IGHD1-20_star_01_13: 0.014705882352941176
+    IGHD1-20_star_01_14: 0.014705882352941176
+    IGHD1-20_star_01_15: 0.014705882352941176
+    IGHD1-20_star_01_16: 0.014705882352941176
+    IGHD1-20_star_01_2: 0.014705882352941176
+    IGHD1-20_star_01_3: 0.029411764705882353
+    IGHD1-20_star_01_4: 0.019607843137254905
+    IGHD1-20_star_01_5: 0.009803921568627454
+    IGHD1-20_star_01_6: 3.2653618371328133e-18
+    IGHD1-20_star_01_7: 0.014705882352941176
+    IGHD1-20_star_01_8: 0.014705882352941176
+    IGHD1-20_star_01_9: 0.014705882352941176
+    insert_left_A: 0.14097744360902253
+    insert_left_C: 0.2537593984962406
+    insert_left_G: 0.17481203007518797
+    insert_left_T: 0.18045112781954886
+- !!python/object:python.hmmwriter.State
+  emissions:
+    probs:
+      A: 0.03526658215056569
+      C: 0.8942002535483029
+      G: 0.03526658215056569
+      T: 0.03526658215056569
+    track: nukes
+  extras:
+    ambiguous_char: N
+    ambiguous_emission_prob: 0.25
+    germline: C
+  name: insert_left_C
+  transitions:
+    IGHD1-20_star_01_0: 0.014705882352941176
+    IGHD1-20_star_01_1: 0.014705882352941176
+    IGHD1-20_star_01_10: 0.014705882352941176
+    IGHD1-20_star_01_11: 0.014705882352941176
+    IGHD1-20_star_01_12: 0.014705882352941176
+    IGHD1-20_star_01_13: 0.014705882352941176
+    IGHD1-20_star_01_14: 0.014705882352941176
+    IGHD1-20_star_01_15: 0.014705882352941176
+    IGHD1-20_star_01_16: 0.014705882352941176
+    IGHD1-20_star_01_2: 0.014705882352941176
+    IGHD1-20_star_01_3: 0.029411764705882353
+    IGHD1-20_star_01_4: 0.019607843137254905
+    IGHD1-20_star_01_5: 0.009803921568627454
+    IGHD1-20_star_01_6: 3.2653618371328133e-18
+    IGHD1-20_star_01_7: 0.014705882352941176
+    IGHD1-20_star_01_8: 0.014705882352941176
+    IGHD1-20_star_01_9: 0.014705882352941176
+    insert_left_A: 0.14097744360902253
+    insert_left_C: 0.2537593984962406
+    insert_left_G: 0.17481203007518797
+    insert_left_T: 0.18045112781954886
+- !!python/object:python.hmmwriter.State
+  emissions:
+    probs:
+      A: 0.03526658215056569
+      C: 0.03526658215056569
+      G: 0.8942002535483029
+      T: 0.03526658215056569
+    track: nukes
+  extras:
+    ambiguous_char: N
+    ambiguous_emission_prob: 0.25
+    germline: G
+  name: insert_left_G
+  transitions:
+    IGHD1-20_star_01_0: 0.014705882352941176
+    IGHD1-20_star_01_1: 0.014705882352941176
+    IGHD1-20_star_01_10: 0.014705882352941176
+    IGHD1-20_star_01_11: 0.014705882352941176
+    IGHD1-20_star_01_12: 0.014705882352941176
+    IGHD1-20_star_01_13: 0.014705882352941176
+    IGHD1-20_star_01_14: 0.014705882352941176
+    IGHD1-20_star_01_15: 0.014705882352941176
+    IGHD1-20_star_01_16: 0.014705882352941176
+    IGHD1-20_star_01_2: 0.014705882352941176
+    IGHD1-20_star_01_3: 0.029411764705882353
+    IGHD1-20_star_01_4: 0.019607843137254905
+    IGHD1-20_star_01_5: 0.009803921568627454
+    IGHD1-20_star_01_6: 3.2653618371328133e-18
+    IGHD1-20_star_01_7: 0.014705882352941176
+    IGHD1-20_star_01_8: 0.014705882352941176
+    IGHD1-20_star_01_9: 0.014705882352941176
+    insert_left_A: 0.14097744360902253
+    insert_left_C: 0.2537593984962406
+    insert_left_G: 0.17481203007518797
+    insert_left_T: 0.18045112781954886
+- !!python/object:python.hmmwriter.State
+  emissions:
+    probs:
+      A: 0.03526658215056569
+      C: 0.03526658215056569
+      G: 0.03526658215056569
+      T: 0.8942002535483029
+    track: nukes
+  extras:
+    ambiguous_char: N
+    ambiguous_emission_prob: 0.25
+    germline: T
+  name: insert_left_T
+  transitions:
+    IGHD1-20_star_01_0: 0.014705882352941176
+    IGHD1-20_star_01_1: 0.014705882352941176
+    IGHD1-20_star_01_10: 0.014705882352941176
+    IGHD1-20_star_01_11: 0.014705882352941176
+    IGHD1-20_star_01_12: 0.014705882352941176
+    IGHD1-20_star_01_13: 0.014705882352941176
+    IGHD1-20_star_01_14: 0.014705882352941176
+    IGHD1-20_star_01_15: 0.014705882352941176
+    IGHD1-20_star_01_16: 0.014705882352941176
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