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.
- bin/partis +1 -1
- bin/partis-test.py +6 -0
- bin/partis.py +1 -1
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/partis-test.py +6 -0
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +645 -127
- python/recombinator.py +2 -0
- python/treegenerator.py +1 -1
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
- test/new-results/annotate-new-simu.yaml +1 -0
- test/new-results/cache-new-partition.csv +59 -0
- test/new-results/get-selection-metrics-new-simu.yaml +1 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
- test/new-results/multi-annotate-new-simu.yaml +1 -0
- test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
- test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
- test/new-results/partition-new-simu/fasttree/iclust-0/log +23 -0
- test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
- test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
- test/new-results/partition-new-simu/fasttree/iclust-1/log +23 -0
- test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
- test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
- test/new-results/partition-new-simu/fasttree/iclust-2/log +22 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
- test/new-results/partition-new-simu.yaml +1 -0
- test/new-results/run-times.csv +9 -0
- test/new-results/seed-partition-new-simu.yaml +1 -0
- test/new-results/test/parameters/data/hmm/all-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/data/hmm/all-mean-n-muted.csv +155 -0
- test/new-results/test/parameters/data/hmm/all-probs.csv +44 -0
- test/new-results/test/parameters/data/hmm/cluster_size.csv +2 -0
- test/new-results/test/parameters/data/hmm/d-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/data/hmm/d-mean-n-muted.csv +14 -0
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+
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22
|
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|
23
|
+
IGHD3-3_star_01_18: 0.017241379310344827
|
|
24
|
+
IGHD3-3_star_01_19: 0.017241379310344827
|
|
25
|
+
IGHD3-3_star_01_2: 0.017241379310344827
|
|
26
|
+
IGHD3-3_star_01_20: 0.017241379310344827
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|
27
|
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IGHD3-3_star_01_21: 0.017241379310344827
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|
28
|
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IGHD3-3_star_01_22: 0.017241379310344827
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|
29
|
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IGHD3-3_star_01_23: 0.017241379310344827
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|
30
|
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IGHD3-3_star_01_24: 0.017241379310344827
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|
31
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32
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33
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IGHD3-3_star_01_27: 0.017241379310344827
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34
|
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IGHD3-3_star_01_28: 0.017241379310344827
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|
35
|
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IGHD3-3_star_01_29: 0.017241379310344827
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|
36
|
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IGHD3-3_star_01_3: 0.017241379310344827
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|
37
|
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IGHD3-3_star_01_30: 0.017241379310344827
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|
38
|
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IGHD3-3_star_01_4: 0.01149425287356322
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|
39
|
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IGHD3-3_star_01_5: 0.005747126436781611
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|
40
|
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IGHD3-3_star_01_6: 1.914177628664063e-18
|
|
41
|
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IGHD3-3_star_01_7: 0.017241379310344827
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|
42
|
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IGHD3-3_star_01_8: 0.017241379310344827
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|
43
|
+
IGHD3-3_star_01_9: 0.017241379310344827
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|
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|
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|
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|
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|
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|
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insert_left_G: 0.11654135338345864
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|
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|
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insert_left_T: 0.12030075187969924
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|
48
|
+
- !!python/object:python.hmmwriter.State
|
|
49
|
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emissions:
|
|
50
|
+
probs:
|
|
51
|
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A: 0.894771606857421
|
|
52
|
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C: 0.03507613104752636
|
|
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G: 0.03507613104752636
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|
54
|
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T: 0.03507613104752636
|
|
55
|
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track: nukes
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|
56
|
+
extras:
|
|
57
|
+
ambiguous_char: N
|
|
58
|
+
ambiguous_emission_prob: 0.25
|
|
59
|
+
germline: A
|
|
60
|
+
name: insert_left_A
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|
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transitions:
|
|
62
|
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|
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IGHD3-3_star_01_1: 0.011494252873563216
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IGHD3-3_star_01_10: 0.011494252873563216
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IGHD3-3_star_01_11: 0.011494252873563216
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IGHD3-3_star_01_13: 0.011494252873563216
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IGHD3-3_star_01_14: 0.011494252873563216
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IGHD3-3_star_01_15: 0.011494252873563216
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|
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IGHD3-3_star_01_16: 0.011494252873563216
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|
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IGHD3-3_star_01_17: 0.011494252873563216
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|
72
|
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IGHD3-3_star_01_18: 0.011494252873563216
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|
73
|
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IGHD3-3_star_01_19: 0.011494252873563216
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|
74
|
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IGHD3-3_star_01_2: 0.011494252873563216
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75
|
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IGHD3-3_star_01_21: 0.011494252873563216
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|
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IGHD3-3_star_01_22: 0.011494252873563216
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|
78
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IGHD3-3_star_01_23: 0.011494252873563216
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IGHD3-3_star_01_24: 0.011494252873563216
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|
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IGHD3-3_star_01_25: 0.011494252873563216
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|
81
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IGHD3-3_star_01_26: 0.011494252873563216
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|
82
|
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IGHD3-3_star_01_27: 0.011494252873563216
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|
83
|
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IGHD3-3_star_01_28: 0.011494252873563216
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|
84
|
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IGHD3-3_star_01_29: 0.011494252873563216
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|
85
|
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IGHD3-3_star_01_3: 0.011494252873563216
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|
86
|
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IGHD3-3_star_01_30: 0.011494252873563216
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|
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|
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IGHD3-3_star_01_4: 0.007662835249042145
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|
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|
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IGHD3-3_star_01_5: 0.003831417624521073
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|
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|
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IGHD3-3_star_01_6: 1.2761184191093751e-18
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|
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|
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IGHD3-3_star_01_7: 0.011494252873563216
|
|
91
|
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IGHD3-3_star_01_8: 0.011494252873563216
|
|
92
|
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IGHD3-3_star_01_9: 0.011494252873563216
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|
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|
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|
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|
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|
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|
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|
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|
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|
97
|
+
- !!python/object:python.hmmwriter.State
|
|
98
|
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emissions:
|
|
99
|
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probs:
|
|
100
|
+
A: 0.03507613104752636
|
|
101
|
+
C: 0.894771606857421
|
|
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|
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G: 0.03507613104752636
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|
103
|
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T: 0.03507613104752636
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|
104
|
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track: nukes
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|
105
|
+
extras:
|
|
106
|
+
ambiguous_char: N
|
|
107
|
+
ambiguous_emission_prob: 0.25
|
|
108
|
+
germline: C
|
|
109
|
+
name: insert_left_C
|
|
110
|
+
transitions:
|
|
111
|
+
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|
|
112
|
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IGHD3-3_star_01_1: 0.011494252873563216
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|
113
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IGHD3-3_star_01_10: 0.011494252873563216
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|
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IGHD3-3_star_01_11: 0.011494252873563216
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|
115
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IGHD3-3_star_01_12: 0.011494252873563216
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|
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IGHD3-3_star_01_13: 0.011494252873563216
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|
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IGHD3-3_star_01_14: 0.011494252873563216
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|
118
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IGHD3-3_star_01_15: 0.011494252873563216
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|
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IGHD3-3_star_01_16: 0.011494252873563216
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|
120
|
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IGHD3-3_star_01_17: 0.011494252873563216
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|
121
|
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IGHD3-3_star_01_18: 0.011494252873563216
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|
122
|
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IGHD3-3_star_01_19: 0.011494252873563216
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|
123
|
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IGHD3-3_star_01_2: 0.011494252873563216
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|
124
|
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IGHD3-3_star_01_20: 0.011494252873563216
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|
125
|
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IGHD3-3_star_01_21: 0.011494252873563216
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|
126
|
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IGHD3-3_star_01_22: 0.011494252873563216
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|
127
|
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IGHD3-3_star_01_23: 0.011494252873563216
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|
128
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IGHD3-3_star_01_24: 0.011494252873563216
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|
129
|
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IGHD3-3_star_01_25: 0.011494252873563216
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|
130
|
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IGHD3-3_star_01_26: 0.011494252873563216
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|
131
|
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IGHD3-3_star_01_27: 0.011494252873563216
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|
132
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IGHD3-3_star_01_28: 0.011494252873563216
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|
133
|
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IGHD3-3_star_01_29: 0.011494252873563216
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|
134
|
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IGHD3-3_star_01_3: 0.011494252873563216
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|
135
|
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IGHD3-3_star_01_30: 0.011494252873563216
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|
136
|
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IGHD3-3_star_01_4: 0.007662835249042145
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|
137
|
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IGHD3-3_star_01_5: 0.003831417624521073
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|
138
|
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IGHD3-3_star_01_6: 1.2761184191093751e-18
|
|
139
|
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IGHD3-3_star_01_7: 0.011494252873563216
|
|
140
|
+
IGHD3-3_star_01_8: 0.011494252873563216
|
|
141
|
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IGHD3-3_star_01_9: 0.011494252873563216
|
|
142
|
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insert_left_A: 0.12531328320802007
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|
143
|
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insert_left_C: 0.2255639097744361
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|
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|
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insert_left_G: 0.15538847117794488
|
|
145
|
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insert_left_T: 0.16040100250626568
|
|
146
|
+
- !!python/object:python.hmmwriter.State
|
|
147
|
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emissions:
|
|
148
|
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probs:
|
|
149
|
+
A: 0.03507613104752636
|
|
150
|
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C: 0.03507613104752636
|
|
151
|
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G: 0.894771606857421
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|
152
|
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T: 0.03507613104752636
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|
153
|
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track: nukes
|
|
154
|
+
extras:
|
|
155
|
+
ambiguous_char: N
|
|
156
|
+
ambiguous_emission_prob: 0.25
|
|
157
|
+
germline: G
|
|
158
|
+
name: insert_left_G
|
|
159
|
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transitions:
|
|
160
|
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|
161
|
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IGHD3-3_star_01_1: 0.011494252873563216
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|
162
|
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IGHD3-3_star_01_10: 0.011494252873563216
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|
163
|
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IGHD3-3_star_01_11: 0.011494252873563216
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|
164
|
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IGHD3-3_star_01_12: 0.011494252873563216
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|
165
|
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IGHD3-3_star_01_13: 0.011494252873563216
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|
166
|
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IGHD3-3_star_01_14: 0.011494252873563216
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|
167
|
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IGHD3-3_star_01_15: 0.011494252873563216
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|
168
|
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IGHD3-3_star_01_16: 0.011494252873563216
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|
169
|
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IGHD3-3_star_01_17: 0.011494252873563216
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|
170
|
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IGHD3-3_star_01_18: 0.011494252873563216
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|
171
|
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IGHD3-3_star_01_19: 0.011494252873563216
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|
172
|
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IGHD3-3_star_01_2: 0.011494252873563216
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|
173
|
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IGHD3-3_star_01_20: 0.011494252873563216
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|
174
|
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IGHD3-3_star_01_21: 0.011494252873563216
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|
175
|
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IGHD3-3_star_01_22: 0.011494252873563216
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|
176
|
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IGHD3-3_star_01_23: 0.011494252873563216
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|
177
|
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IGHD3-3_star_01_24: 0.011494252873563216
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|
178
|
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IGHD3-3_star_01_25: 0.011494252873563216
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|
179
|
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IGHD3-3_star_01_26: 0.011494252873563216
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|
180
|
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IGHD3-3_star_01_27: 0.011494252873563216
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|
181
|
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IGHD3-3_star_01_28: 0.011494252873563216
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|
182
|
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IGHD3-3_star_01_29: 0.011494252873563216
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|
183
|
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IGHD3-3_star_01_3: 0.011494252873563216
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|
184
|
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IGHD3-3_star_01_30: 0.011494252873563216
|
|
185
|
+
IGHD3-3_star_01_4: 0.007662835249042145
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|
186
|
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IGHD3-3_star_01_5: 0.003831417624521073
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|
187
|
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IGHD3-3_star_01_6: 1.2761184191093751e-18
|
|
188
|
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IGHD3-3_star_01_7: 0.011494252873563216
|
|
189
|
+
IGHD3-3_star_01_8: 0.011494252873563216
|
|
190
|
+
IGHD3-3_star_01_9: 0.011494252873563216
|
|
191
|
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insert_left_A: 0.12531328320802007
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|
192
|
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insert_left_C: 0.2255639097744361
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|
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|
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insert_left_G: 0.15538847117794488
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|
194
|
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insert_left_T: 0.16040100250626568
|
|
195
|
+
- !!python/object:python.hmmwriter.State
|
|
196
|
+
emissions:
|
|
197
|
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probs:
|
|
198
|
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A: 0.03507613104752636
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|
199
|
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C: 0.03507613104752636
|
|
200
|
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G: 0.03507613104752636
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|
201
|
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T: 0.894771606857421
|
|
202
|
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track: nukes
|
|
203
|
+
extras:
|
|
204
|
+
ambiguous_char: N
|
|
205
|
+
ambiguous_emission_prob: 0.25
|
|
206
|
+
germline: T
|
|
207
|
+
name: insert_left_T
|
|
208
|
+
transitions:
|
|
209
|
+
IGHD3-3_star_01_0: 0.011494252873563216
|
|
210
|
+
IGHD3-3_star_01_1: 0.011494252873563216
|
|
211
|
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IGHD3-3_star_01_10: 0.011494252873563216
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|
212
|
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IGHD3-3_star_01_11: 0.011494252873563216
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|
213
|
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IGHD3-3_star_01_12: 0.011494252873563216
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|
214
|
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IGHD3-3_star_01_13: 0.011494252873563216
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|
215
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IGHD3-3_star_01_14: 0.011494252873563216
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|
216
|
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IGHD3-3_star_01_15: 0.011494252873563216
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|
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|
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IGHD3-3_star_01_16: 0.011494252873563216
|
|
218
|
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IGHD3-3_star_01_17: 0.011494252873563216
|
|
219
|
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IGHD3-3_star_01_18: 0.011494252873563216
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|
220
|
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IGHD3-3_star_01_19: 0.011494252873563216
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|
221
|
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IGHD3-3_star_01_2: 0.011494252873563216
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|
222
|
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IGHD3-3_star_01_20: 0.011494252873563216
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|
223
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IGHD3-3_star_01_21: 0.011494252873563216
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|
224
|
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IGHD3-3_star_01_22: 0.011494252873563216
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|
225
|
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IGHD3-3_star_01_23: 0.011494252873563216
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|
226
|
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IGHD3-3_star_01_24: 0.011494252873563216
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|
227
|
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IGHD3-3_star_01_25: 0.011494252873563216
|
|
228
|
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IGHD3-3_star_01_26: 0.011494252873563216
|
|
229
|
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IGHD3-3_star_01_27: 0.011494252873563216
|
|
230
|
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IGHD3-3_star_01_28: 0.011494252873563216
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|
231
|
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IGHD3-3_star_01_29: 0.011494252873563216
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|
232
|
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IGHD3-3_star_01_3: 0.011494252873563216
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|
233
|
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IGHD3-3_star_01_30: 0.011494252873563216
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|
234
|
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IGHD3-3_star_01_4: 0.007662835249042145
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|
235
|
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IGHD3-3_star_01_5: 0.003831417624521073
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|
236
|
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IGHD3-3_star_01_6: 1.2761184191093751e-18
|
|
237
|
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IGHD3-3_star_01_7: 0.011494252873563216
|
|
238
|
+
IGHD3-3_star_01_8: 0.011494252873563216
|
|
239
|
+
IGHD3-3_star_01_9: 0.011494252873563216
|
|
240
|
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|
241
|
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insert_left_C: 0.2255639097744361
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|
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|
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insert_left_G: 0.15538847117794488
|
|
243
|
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insert_left_T: 0.16040100250626568
|
|
244
|
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- !!python/object:python.hmmwriter.State
|
|
245
|
+
emissions:
|
|
246
|
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probs:
|
|
247
|
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A: 0.035076131047526354
|
|
248
|
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C: 0.035076131047526354
|
|
249
|
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G: 0.894771606857421
|
|
250
|
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T: 0.035076131047526354
|
|
251
|
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track: nukes
|
|
252
|
+
extras:
|
|
253
|
+
ambiguous_char: N
|
|
254
|
+
ambiguous_emission_prob: 0.25
|
|
255
|
+
germline: G
|
|
256
|
+
name: IGHD3-3_star_01_0
|
|
257
|
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transitions:
|
|
258
|
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IGHD3-3_star_01_1: 0.9636363636363636
|
|
259
|
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end: 0.03636363636363636
|
|
260
|
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- !!python/object:python.hmmwriter.State
|
|
261
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581
|
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|
|
582
|
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|
583
|
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|
584
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|
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|
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|
589
|
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|
590
|
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|
591
|
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|
592
|
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|
593
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|
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- !!python/object:python.hmmwriter.State
|
|
597
|
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|
|
598
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|
599
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|
600
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|
601
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|
602
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|
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|
605
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|
606
|
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|
607
|
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germline: T
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|
608
|
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|
609
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610
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|
611
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|
612
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- !!python/object:python.hmmwriter.State
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|
613
|
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|
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|
615
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|
616
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|
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G: 0.03372062171426512
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|
618
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T: 0.03372062171426512
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|
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620
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|
621
|
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|
622
|
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|
|
623
|
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|
624
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|
625
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626
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|
627
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628
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- !!python/object:python.hmmwriter.State
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|
629
|
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|
630
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|
631
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634
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635
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636
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|
637
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|
638
|
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|
639
|
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germline: T
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|
640
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|
641
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|
642
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|
643
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- !!python/object:python.hmmwriter.State
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|
645
|
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|
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649
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G: 0.0341079100951969
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653
|
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|
654
|
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|
655
|
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germline: T
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|
656
|
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|
657
|
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|
|
658
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IGHD3-3_star_01_26: 0.9636363636363636
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|
659
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|
660
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- !!python/object:python.hmmwriter.State
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|
661
|
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|
662
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|
663
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|
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|
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|
669
|
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|
670
|
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|
|
671
|
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germline: A
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|
672
|
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|
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|
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|
674
|
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|
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|
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- !!python/object:python.hmmwriter.State
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|
677
|
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|
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|
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|
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|
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|
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|
685
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|
686
|
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|
687
|
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germline: T
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|
688
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|
689
|
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|
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|
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|
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- !!python/object:python.hmmwriter.State
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|
693
|
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|
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|
695
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|
696
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|
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T: 0.034688842666594576
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|
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|
700
|
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extras:
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|
701
|
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|
702
|
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|
|
703
|
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germline: A
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|
704
|
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|
705
|
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706
|
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|
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- !!python/object:python.hmmwriter.State
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|
709
|
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|
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|
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|
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G: 0.03488248685706047
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
719
|
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germline: C
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|
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|
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|
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|
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|
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|
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|
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|
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|
724
|
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- !!python/object:python.hmmwriter.State
|
|
725
|
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|
726
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
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|
734
|
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|
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germline: C
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|
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|
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|
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|
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|
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|
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|
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nukes:
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|
741
|
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- A
|
|
742
|
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- C
|
|
743
|
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- G
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|
744
|
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- T
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