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
- test/new-results/test/parameters/data/hmm/d_gene-d_3p_del-probs.csv +34 -0
- test/new-results/test/parameters/data/hmm/d_gene-d_5p_del-probs.csv +42 -0
- test/new-results/test/parameters/data/hmm/d_gene-probs.csv +20 -0
- test/new-results/test/parameters/data/hmm/d_gene-vd_insertion-probs.csv +39 -0
- test/new-results/test/parameters/data/hmm/dj_insertion_content.csv +5 -0
- test/new-results/test/parameters/data/hmm/fv_insertion-probs.csv +4 -0
- test/new-results/test/parameters/data/hmm/germline-sets/igh/extras.csv +23 -0
- test/new-results/test/parameters/data/hmm/germline-sets/igh/ighd.fasta +38 -0
- test/new-results/test/parameters/data/hmm/germline-sets/igh/ighj.fasta +14 -0
- test/new-results/test/parameters/data/hmm/germline-sets/igh/ighv.fasta +30 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD1-20_star_01.yaml +449 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD1-26_star_01.yaml +512 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD2-15_star_01.yaml +743 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD2-21_star_01.yaml +681 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD2-21_star_02.yaml +681 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD2-2_star_01.yaml +743 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD2-8_star_01.yaml +744 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD2-8_star_02.yaml +743 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD3-10_star_01.yaml +743 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD3-10_star_03.yaml +744 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD3-16_star_02.yaml +870 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD3-22_star_01.yaml +743 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD3-3_star_01.yaml +744 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD4-17_star_01.yaml +429 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD4-4_star_01.yaml +428 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD5-5_star_01.yaml +513 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD6-13_star_01.yaml +533 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD6-19_star_01.yaml +534 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHD6-6_star_01.yaml +470 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHJ1_star_01.yaml +986 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHJ2_star_01.yaml +1006 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHJ3_star_02.yaml +946 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHJ4_star_02.yaml +906 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHJ5_star_02.yaml +966 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHJ6_star_02.yaml +1206 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHJ6_star_03.yaml +1206 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV1-18_star_01.yaml +4484 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV1-2_star_02.yaml +4484 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV2-5_star_02.yaml +4560 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV2-70D_star_04.yaml +4561 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV3-11_star_04.yaml +4484 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV3-23_star_01.yaml +4484 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV3-66_star_02.yaml +4439 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV3-69-1_star_02.yaml +4439 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV3-7_star_05.yaml +4484 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV3-9_star_02.yaml +4516 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV4-34_star_01.yaml +4439 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV4-39_star_09.yaml +4529 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV4-4_star_09.yaml +4438 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV4-61_star_01.yaml +4529 -0
- test/new-results/test/parameters/data/hmm/hmms/IGHV5-51_star_01.yaml +4484 -0
- test/new-results/test/parameters/data/hmm/j-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/data/hmm/j-mean-n-muted.csv +25 -0
- test/new-results/test/parameters/data/hmm/j_gene-dj_insertion-probs.csv +31 -0
- test/new-results/test/parameters/data/hmm/j_gene-j_3p_del-probs.csv +8 -0
- test/new-results/test/parameters/data/hmm/j_gene-j_5p_del-probs.csv +31 -0
- test/new-results/test/parameters/data/hmm/j_gene-probs.csv +8 -0
- test/new-results/test/parameters/data/hmm/jf_insertion-probs.csv +3 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD1-20_star_01.csv +8 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD1-26_star_01.csv +8 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-15_star_01.csv +32 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-21_star_01.csv +17 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-21_star_02.csv +29 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-2_star_01.csv +10 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-8_star_01.csv +32 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD2-8_star_02.csv +9 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD3-10_star_01.csv +27 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD3-10_star_03.csv +14 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD3-16_star_02.csv +35 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD3-22_star_01.csv +32 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD3-3_star_01.csv +21 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD4-17_star_01.csv +12 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD4-4_star_01.csv +12 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD5-5_star_01.csv +13 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD6-13_star_01.csv +22 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD6-19_star_01.csv +22 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHD6-6_star_01.csv +19 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ1_star_01.csv +52 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ2_star_01.csv +54 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ3_star_02.csv +51 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ4_star_02.csv +49 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ5_star_02.csv +50 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ6_star_02.csv +33 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHJ6_star_03.csv +40 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV1-18_star_01.csv +297 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV1-2_star_02.csv +296 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV2-5_star_02.csv +66 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV2-70D_star_04.csv +89 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-11_star_04.csv +73 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-23_star_01.csv +297 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-66_star_02.csv +294 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-69-1_star_02.csv +38 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-7_star_05.csv +70 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV3-9_star_02.csv +40 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV4-34_star_01.csv +40 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV4-39_star_09.csv +40 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV4-4_star_09.csv +59 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV4-61_star_01.csv +300 -0
- test/new-results/test/parameters/data/hmm/mute-freqs/IGHV5-51_star_01.csv +296 -0
- test/new-results/test/parameters/data/hmm/seq_content.csv +5 -0
- test/new-results/test/parameters/data/hmm/v-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/data/hmm/v-mean-n-muted.csv +122 -0
- test/new-results/test/parameters/data/hmm/v_gene-probs.csv +16 -0
- test/new-results/test/parameters/data/hmm/v_gene-v_3p_del-probs.csv +24 -0
- test/new-results/test/parameters/data/hmm/v_gene-v_5p_del-probs.csv +16 -0
- test/new-results/test/parameters/data/hmm/vd_insertion_content.csv +5 -0
- test/new-results/test/parameters/data/sw/all-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/data/sw/all-mean-n-muted.csv +155 -0
- test/new-results/test/parameters/data/sw/all-probs.csv +44 -0
- test/new-results/test/parameters/data/sw/cluster_size.csv +2 -0
- test/new-results/test/parameters/data/sw/d-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/data/sw/d-mean-n-muted.csv +14 -0
- test/new-results/test/parameters/data/sw/d_gene-d_3p_del-probs.csv +40 -0
- test/new-results/test/parameters/data/sw/d_gene-d_5p_del-probs.csv +42 -0
- test/new-results/test/parameters/data/sw/d_gene-probs.csv +23 -0
- test/new-results/test/parameters/data/sw/d_gene-vd_insertion-probs.csv +40 -0
- test/new-results/test/parameters/data/sw/dj_insertion_content.csv +5 -0
- test/new-results/test/parameters/data/sw/fv_insertion-probs.csv +3 -0
- test/new-results/test/parameters/data/sw/germline-sets/igh/extras.csv +26 -0
- test/new-results/test/parameters/data/sw/germline-sets/igh/ighd.fasta +44 -0
- test/new-results/test/parameters/data/sw/germline-sets/igh/ighj.fasta +14 -0
- test/new-results/test/parameters/data/sw/germline-sets/igh/ighv.fasta +36 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD1-1_star_01.yaml +450 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD1-20_star_01.yaml +449 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD1-26_star_01.yaml +512 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD2-15_star_01.yaml +744 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD2-21_star_01.yaml +681 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD2-21_star_02.yaml +681 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD2-2_star_01.yaml +743 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD2-8_star_01.yaml +744 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD2-8_star_02.yaml +743 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD3-10_star_01.yaml +743 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD3-10_star_03.yaml +744 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD3-16_star_02.yaml +869 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD3-16_star_03.yaml +869 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD3-22_star_01.yaml +743 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD3-3_star_01.yaml +744 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD4-17_star_01.yaml +429 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD4-4_star_01.yaml +428 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD5-5_star_01.yaml +513 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD6-13_star_01.yaml +533 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD6-19_star_01.yaml +533 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD6-25_star_01.yaml +470 -0
- test/new-results/test/parameters/data/sw/hmms/IGHD6-6_star_01.yaml +470 -0
- test/new-results/test/parameters/data/sw/hmms/IGHJ1_star_01.yaml +986 -0
- test/new-results/test/parameters/data/sw/hmms/IGHJ2_star_01.yaml +1006 -0
- test/new-results/test/parameters/data/sw/hmms/IGHJ3_star_02.yaml +946 -0
- test/new-results/test/parameters/data/sw/hmms/IGHJ4_star_02.yaml +906 -0
- test/new-results/test/parameters/data/sw/hmms/IGHJ5_star_02.yaml +966 -0
- test/new-results/test/parameters/data/sw/hmms/IGHJ6_star_02.yaml +1206 -0
- test/new-results/test/parameters/data/sw/hmms/IGHJ6_star_03.yaml +1206 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV1-18_star_01.yaml +4484 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV1-2_star_02.yaml +4484 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV2-5_star_02.yaml +4560 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV2-70D_star_04.yaml +4561 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV3-11_star_04.yaml +4484 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV3-23_star_01.yaml +4484 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV3-23_star_03.yaml +4484 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV3-30_star_04.yaml +4484 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV3-48_star_03.yaml +4484 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV3-66_star_02.yaml +4439 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV3-69-1_star_02.yaml +4439 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV3-7_star_05.yaml +4484 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV3-9_star_02.yaml +4516 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV4-34_star_01.yaml +4439 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV4-39_star_09.yaml +4529 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV4-4_star_09.yaml +4438 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV4-61_star_01.yaml +4529 -0
- test/new-results/test/parameters/data/sw/hmms/IGHV5-51_star_01.yaml +4484 -0
- test/new-results/test/parameters/data/sw/j-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/data/sw/j-mean-n-muted.csv +25 -0
- test/new-results/test/parameters/data/sw/j_gene-dj_insertion-probs.csv +32 -0
- test/new-results/test/parameters/data/sw/j_gene-j_3p_del-probs.csv +11 -0
- test/new-results/test/parameters/data/sw/j_gene-j_5p_del-probs.csv +31 -0
- test/new-results/test/parameters/data/sw/j_gene-probs.csv +8 -0
- test/new-results/test/parameters/data/sw/jf_insertion-probs.csv +3 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD1-1_star_01.csv +4 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD1-20_star_01.csv +8 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD1-26_star_01.csv +8 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-15_star_01.csv +32 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-21_star_01.csv +28 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-21_star_02.csv +27 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-2_star_01.csv +27 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-8_star_01.csv +32 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD2-8_star_02.csv +12 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-10_star_01.csv +29 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-10_star_03.csv +14 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-16_star_02.csv +34 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-16_star_03.csv +20 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-22_star_01.csv +30 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD3-3_star_01.csv +21 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD4-17_star_01.csv +12 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD4-4_star_01.csv +9 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD5-5_star_01.csv +9 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD6-13_star_01.csv +20 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD6-19_star_01.csv +21 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD6-25_star_01.csv +12 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHD6-6_star_01.csv +19 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHJ1_star_01.csv +52 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHJ2_star_01.csv +54 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHJ3_star_02.csv +51 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHJ4_star_02.csv +49 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHJ5_star_02.csv +51 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHJ6_star_02.csv +33 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHJ6_star_03.csv +40 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV1-18_star_01.csv +297 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV1-2_star_02.csv +296 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV2-5_star_02.csv +66 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV2-70D_star_04.csv +89 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-11_star_04.csv +73 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-23_star_01.csv +297 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-23_star_03.csv +32 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-30_star_04.csv +38 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-48_star_03.csv +38 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-66_star_02.csv +292 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-69-1_star_02.csv +38 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-7_star_05.csv +70 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV3-9_star_02.csv +40 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV4-34_star_01.csv +40 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV4-39_star_09.csv +40 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV4-4_star_09.csv +59 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV4-61_star_01.csv +300 -0
- test/new-results/test/parameters/data/sw/mute-freqs/IGHV5-51_star_01.csv +296 -0
- test/new-results/test/parameters/data/sw/seq_content.csv +5 -0
- test/new-results/test/parameters/data/sw/v-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/data/sw/v-mean-n-muted.csv +122 -0
- test/new-results/test/parameters/data/sw/v_gene-probs.csv +19 -0
- test/new-results/test/parameters/data/sw/v_gene-v_3p_del-probs.csv +25 -0
- test/new-results/test/parameters/data/sw/v_gene-v_5p_del-probs.csv +29 -0
- test/new-results/test/parameters/data/sw/vd_insertion_content.csv +5 -0
- test/new-results/test/parameters/data/sw-cache.yaml +1 -0
- test/new-results/test/parameters/simu/hmm/all-mean-mute-freqs.csv +3 -3
- test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv +11 -11
- test/new-results/test/parameters/simu/hmm/all-probs.csv +13 -3
- test/new-results/test/parameters/simu/hmm/cluster_size.csv +1 -1
- test/new-results/test/parameters/simu/hmm/d-mean-mute-freqs.csv +6 -6
- test/new-results/test/parameters/simu/hmm/d-mean-n-muted.csv +3 -3
- test/new-results/test/parameters/simu/hmm/d_gene-d_3p_del-probs.csv +6 -1
- test/new-results/test/parameters/simu/hmm/d_gene-d_5p_del-probs.csv +9 -2
- test/new-results/test/parameters/simu/hmm/d_gene-probs.csv +5 -1
- test/new-results/test/parameters/simu/hmm/d_gene-vd_insertion-probs.csv +10 -2
- test/new-results/test/parameters/simu/hmm/dj_insertion_content.csv +4 -4
- test/new-results/test/parameters/simu/hmm/fv_insertion-probs.csv +3 -2
- test/new-results/test/parameters/simu/hmm/germline-sets/igh/extras.csv +6 -0
- test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighd.fasta +8 -0
- test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighj.fasta +2 -0
- test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighv.fasta +10 -0
- test/new-results/test/parameters/simu/hmm/hmms/IGHD1-20_star_01.yaml +449 -0
- test/new-results/test/parameters/simu/hmm/hmms/IGHD3-16_star_02.yaml +870 -0
- test/new-results/test/parameters/simu/hmm/hmms/IGHD3-22_star_01.yaml +744 -0
- test/new-results/test/parameters/simu/hmm/hmms/IGHD6-13_star_01.yaml +267 -268
- test/new-results/test/parameters/simu/hmm/hmms/IGHD6-19_star_01.yaml +534 -0
- test/new-results/test/parameters/simu/hmm/hmms/IGHJ1_star_01.yaml +986 -0
- test/new-results/test/parameters/simu/hmm/hmms/IGHJ4_star_02.yaml +306 -306
- test/new-results/test/parameters/simu/hmm/hmms/IGHJ6_star_02.yaml +284 -284
- test/new-results/test/parameters/simu/hmm/hmms/IGHV1-18_star_01.yaml +4484 -0
- test/new-results/test/parameters/simu/hmm/hmms/IGHV3-23_star_01.yaml +4484 -0
- test/new-results/test/parameters/simu/hmm/hmms/IGHV3-66_star_02.yaml +1191 -1191
- test/new-results/test/parameters/simu/hmm/hmms/IGHV3-7_star_05.yaml +2 -2
- test/new-results/test/parameters/simu/hmm/hmms/IGHV4-4_star_09.yaml +4438 -0
- test/new-results/test/parameters/simu/hmm/hmms/IGHV4-61_star_01.yaml +4529 -0
- test/new-results/test/parameters/simu/hmm/hmms/IGHV5-51_star_01.yaml +4484 -0
- test/new-results/test/parameters/simu/hmm/j-mean-mute-freqs.csv +5 -5
- test/new-results/test/parameters/simu/hmm/j-mean-n-muted.csv +4 -4
- test/new-results/test/parameters/simu/hmm/j_gene-dj_insertion-probs.csv +9 -2
- test/new-results/test/parameters/simu/hmm/j_gene-j_3p_del-probs.csv +2 -1
- test/new-results/test/parameters/simu/hmm/j_gene-j_5p_del-probs.csv +7 -2
- test/new-results/test/parameters/simu/hmm/j_gene-probs.csv +2 -1
- test/new-results/test/parameters/simu/hmm/jf_insertion-probs.csv +1 -1
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD1-20_star_01.csv +9 -0
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-16_star_02.csv +30 -0
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-22_star_01.csv +32 -0
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-13_star_01.csv +16 -13
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-19_star_01.csv +22 -0
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ1_star_01.csv +50 -0
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ4_star_02.csv +44 -40
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ6_star_02.csv +2 -0
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV1-18_star_01.csv +297 -0
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-23_star_01.csv +297 -0
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-66_star_02.csv +293 -291
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-4_star_09.csv +291 -0
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-61_star_01.csv +300 -0
- test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV5-51_star_01.csv +296 -0
- test/new-results/test/parameters/simu/hmm/seq_content.csv +4 -4
- test/new-results/test/parameters/simu/hmm/v-mean-mute-freqs.csv +3 -3
- test/new-results/test/parameters/simu/hmm/v-mean-n-muted.csv +7 -7
- test/new-results/test/parameters/simu/hmm/v_gene-probs.csv +6 -1
- test/new-results/test/parameters/simu/hmm/v_gene-v_3p_del-probs.csv +7 -1
- test/new-results/test/parameters/simu/hmm/v_gene-v_5p_del-probs.csv +6 -1
- test/new-results/test/parameters/simu/hmm/vd_insertion_content.csv +4 -4
- test/new-results/test/parameters/simu/sw/all-mean-mute-freqs.csv +3 -3
- test/new-results/test/parameters/simu/sw/all-mean-n-muted.csv +8 -8
- test/new-results/test/parameters/simu/sw/all-probs.csv +9 -1
- test/new-results/test/parameters/simu/sw/cluster_size.csv +1 -1
- test/new-results/test/parameters/simu/sw/d-mean-mute-freqs.csv +5 -5
- test/new-results/test/parameters/simu/sw/d-mean-n-muted.csv +3 -3
- test/new-results/test/parameters/simu/sw/d_gene-d_3p_del-probs.csv +7 -1
- test/new-results/test/parameters/simu/sw/d_gene-d_5p_del-probs.csv +7 -1
- test/new-results/test/parameters/simu/sw/d_gene-probs.csv +5 -1
- test/new-results/test/parameters/simu/sw/d_gene-vd_insertion-probs.csv +8 -1
- test/new-results/test/parameters/simu/sw/dj_insertion_content.csv +4 -4
- test/new-results/test/parameters/simu/sw/fv_insertion-probs.csv +1 -1
- test/new-results/test/parameters/simu/sw/germline-sets/igh/extras.csv +6 -0
- test/new-results/test/parameters/simu/sw/germline-sets/igh/ighd.fasta +8 -0
- test/new-results/test/parameters/simu/sw/germline-sets/igh/ighj.fasta +2 -0
- test/new-results/test/parameters/simu/sw/germline-sets/igh/ighv.fasta +10 -0
- test/new-results/test/parameters/simu/sw/hmms/IGHD1-20_star_01.yaml +449 -0
- test/new-results/test/parameters/simu/sw/hmms/IGHD3-16_star_02.yaml +870 -0
- test/new-results/test/parameters/simu/sw/hmms/IGHD3-22_star_01.yaml +744 -0
- test/new-results/test/parameters/simu/sw/hmms/IGHD6-13_star_01.yaml +267 -268
- test/new-results/test/parameters/simu/sw/hmms/IGHD6-19_star_01.yaml +534 -0
- test/new-results/test/parameters/simu/sw/hmms/IGHJ1_star_01.yaml +986 -0
- test/new-results/test/parameters/simu/sw/hmms/IGHJ4_star_02.yaml +306 -306
- test/new-results/test/parameters/simu/sw/hmms/IGHJ6_star_02.yaml +22 -22
- test/new-results/test/parameters/simu/sw/hmms/IGHV1-18_star_01.yaml +4484 -0
- test/new-results/test/parameters/simu/sw/hmms/IGHV3-23_star_01.yaml +4484 -0
- test/new-results/test/parameters/simu/sw/hmms/IGHV3-66_star_02.yaml +1191 -1191
- test/new-results/test/parameters/simu/sw/hmms/IGHV3-7_star_05.yaml +2 -2
- test/new-results/test/parameters/simu/sw/hmms/IGHV4-4_star_09.yaml +4438 -0
- test/new-results/test/parameters/simu/sw/hmms/IGHV4-61_star_01.yaml +4529 -0
- test/new-results/test/parameters/simu/sw/hmms/IGHV5-51_star_01.yaml +4484 -0
- test/new-results/test/parameters/simu/sw/j-mean-mute-freqs.csv +4 -4
- test/new-results/test/parameters/simu/sw/j-mean-n-muted.csv +3 -3
- test/new-results/test/parameters/simu/sw/j_gene-dj_insertion-probs.csv +7 -1
- test/new-results/test/parameters/simu/sw/j_gene-j_3p_del-probs.csv +2 -1
- test/new-results/test/parameters/simu/sw/j_gene-j_5p_del-probs.csv +7 -1
- test/new-results/test/parameters/simu/sw/j_gene-probs.csv +2 -1
- test/new-results/test/parameters/simu/sw/jf_insertion-probs.csv +1 -1
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHD1-20_star_01.csv +9 -0
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-16_star_02.csv +30 -0
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-22_star_01.csv +32 -0
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-13_star_01.csv +16 -13
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-19_star_01.csv +20 -0
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ1_star_01.csv +50 -0
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ4_star_02.csv +48 -40
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHV1-18_star_01.csv +297 -0
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-23_star_01.csv +297 -0
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv +293 -291
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-4_star_09.csv +291 -0
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-61_star_01.csv +300 -0
- test/new-results/test/parameters/simu/sw/mute-freqs/IGHV5-51_star_01.csv +296 -0
- test/new-results/test/parameters/simu/sw/seq_content.csv +4 -4
- test/new-results/test/parameters/simu/sw/v-mean-mute-freqs.csv +3 -3
- test/new-results/test/parameters/simu/sw/v-mean-n-muted.csv +7 -7
- test/new-results/test/parameters/simu/sw/v_gene-probs.csv +6 -1
- test/new-results/test/parameters/simu/sw/v_gene-v_3p_del-probs.csv +7 -1
- test/new-results/test/parameters/simu/sw/v_gene-v_5p_del-probs.csv +6 -1
- test/new-results/test/parameters/simu/sw/vd_insertion_content.csv +4 -4
- test/new-results/test/parameters/simu/sw-cache.yaml +1 -1
- test/new-results/test/parameters/simu/true/all-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/simu/true/all-mean-n-muted.csv +155 -0
- test/new-results/test/parameters/simu/true/all-probs.csv +10 -0
- test/new-results/test/parameters/simu/true/cluster_size.csv +7 -0
- test/new-results/test/parameters/simu/true/d-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/simu/true/d-mean-n-muted.csv +14 -0
- test/new-results/test/parameters/simu/true/d_gene-d_3p_del-probs.csv +9 -0
- test/new-results/test/parameters/simu/true/d_gene-d_5p_del-probs.csv +10 -0
- test/new-results/test/parameters/simu/true/d_gene-probs.csv +7 -0
- test/new-results/test/parameters/simu/true/d_gene-vd_insertion-probs.csv +10 -0
- test/new-results/test/parameters/simu/true/dj_insertion_content.csv +5 -0
- test/new-results/test/parameters/simu/true/fv_insertion-probs.csv +2 -0
- test/new-results/test/parameters/simu/true/germline-sets/igh/extras.csv +11 -0
- test/new-results/test/parameters/simu/true/germline-sets/igh/ighd.fasta +12 -0
- test/new-results/test/parameters/simu/true/germline-sets/igh/ighj.fasta +6 -0
- test/new-results/test/parameters/simu/true/germline-sets/igh/ighv.fasta +14 -0
- test/new-results/test/parameters/simu/true/j-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/simu/true/j-mean-n-muted.csv +25 -0
- test/new-results/test/parameters/simu/true/j_gene-dj_insertion-probs.csv +7 -0
- test/new-results/test/parameters/simu/true/j_gene-j_3p_del-probs.csv +4 -0
- test/new-results/test/parameters/simu/true/j_gene-j_5p_del-probs.csv +9 -0
- test/new-results/test/parameters/simu/true/j_gene-probs.csv +4 -0
- test/new-results/test/parameters/simu/true/jf_insertion-probs.csv +2 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHD1-20_star_01.csv +8 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHD3-16_star_02.csv +30 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHD3-22_star_01.csv +32 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHD6-13_star_01.csv +22 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHD6-19_star_01.csv +22 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHD6-6_star_01.csv +13 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHJ1_star_01.csv +50 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHJ4_star_02.csv +45 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHJ6_star_02.csv +47 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHV1-18_star_01.csv +297 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHV3-23_star_01.csv +297 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHV3-66_star_02.csv +294 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHV3-7_star_05.csv +297 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-4_star_09.csv +291 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-61_star_01.csv +300 -0
- test/new-results/test/parameters/simu/true/mute-freqs/IGHV5-51_star_01.csv +296 -0
- test/new-results/test/parameters/simu/true/seq_content.csv +5 -0
- test/new-results/test/parameters/simu/true/v-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/simu/true/v-mean-n-muted.csv +122 -0
- test/new-results/test/parameters/simu/true/v_gene-probs.csv +8 -0
- test/new-results/test/parameters/simu/true/v_gene-v_3p_del-probs.csv +9 -0
- test/new-results/test/parameters/simu/true/v_gene-v_5p_del-probs.csv +8 -0
- test/new-results/test/parameters/simu/true/vd_insertion_content.csv +5 -0
- test/new-results/test.log +203 -24
- test/new-results/vsearch-partition-new-simu.yaml +1 -0
- test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
- test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +5 -5
- test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +2 -2
- test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +1 -1
- test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
- test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
- test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
- test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
- test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
- test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
- test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
- test/paired/new-results/run-times.csv +6 -6
- test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +43 -43
- test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +40 -40
- test/paired/new-results/subset-partition-new-simu/merged-partition.log +25 -25
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
- test/paired/new-results/test.log +135 -135
- test/test.py +6 -0
- test/trees.nwk +100 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/top_level.txt +0 -0
|
@@ -0,0 +1,743 @@
|
|
|
1
|
+
!!python/object:python.hmmwriter.HMM
|
|
2
|
+
extras:
|
|
3
|
+
gene_prob: 0.021739130434782608
|
|
4
|
+
overall_mute_freq: 0.08956521739130437
|
|
5
|
+
per_gene_mute_freq: 0.10285985998960487
|
|
6
|
+
name: IGHD2-8_star_02
|
|
7
|
+
states:
|
|
8
|
+
- !!python/object:python.hmmwriter.State
|
|
9
|
+
emissions: null
|
|
10
|
+
extras: {}
|
|
11
|
+
name: init
|
|
12
|
+
transitions:
|
|
13
|
+
IGHD2-8_star_02_0: 0.0196078431372549
|
|
14
|
+
IGHD2-8_star_02_1: 0.0196078431372549
|
|
15
|
+
IGHD2-8_star_02_10: 0.0196078431372549
|
|
16
|
+
IGHD2-8_star_02_11: 0.01764705882352941
|
|
17
|
+
IGHD2-8_star_02_12: 0.01568627450980392
|
|
18
|
+
IGHD2-8_star_02_13: 0.013725490196078433
|
|
19
|
+
IGHD2-8_star_02_14: 0.011764705882352943
|
|
20
|
+
IGHD2-8_star_02_15: 0.009803921568627453
|
|
21
|
+
IGHD2-8_star_02_16: 0.007843137254901964
|
|
22
|
+
IGHD2-8_star_02_17: 0.005882352941176474
|
|
23
|
+
IGHD2-8_star_02_18: 0.003921568627450983
|
|
24
|
+
IGHD2-8_star_02_19: 0.001960784313725493
|
|
25
|
+
IGHD2-8_star_02_2: 0.0196078431372549
|
|
26
|
+
IGHD2-8_star_02_20: 2.7211348642773444e-18
|
|
27
|
+
IGHD2-8_star_02_21: 0.0196078431372549
|
|
28
|
+
IGHD2-8_star_02_22: 0.0196078431372549
|
|
29
|
+
IGHD2-8_star_02_23: 0.0196078431372549
|
|
30
|
+
IGHD2-8_star_02_24: 0.0196078431372549
|
|
31
|
+
IGHD2-8_star_02_25: 0.0196078431372549
|
|
32
|
+
IGHD2-8_star_02_26: 0.0196078431372549
|
|
33
|
+
IGHD2-8_star_02_27: 0.0196078431372549
|
|
34
|
+
IGHD2-8_star_02_28: 0.0196078431372549
|
|
35
|
+
IGHD2-8_star_02_29: 0.0196078431372549
|
|
36
|
+
IGHD2-8_star_02_3: 0.0196078431372549
|
|
37
|
+
IGHD2-8_star_02_30: 0.0196078431372549
|
|
38
|
+
IGHD2-8_star_02_4: 0.0196078431372549
|
|
39
|
+
IGHD2-8_star_02_5: 0.0196078431372549
|
|
40
|
+
IGHD2-8_star_02_6: 0.0196078431372549
|
|
41
|
+
IGHD2-8_star_02_7: 0.0196078431372549
|
|
42
|
+
IGHD2-8_star_02_8: 0.0196078431372549
|
|
43
|
+
IGHD2-8_star_02_9: 0.0196078431372549
|
|
44
|
+
insert_left_A: 0.09854014598540146
|
|
45
|
+
insert_left_C: 0.16970802919708028
|
|
46
|
+
insert_left_G: 0.10948905109489052
|
|
47
|
+
insert_left_T: 0.12226277372262774
|
|
48
|
+
- !!python/object:python.hmmwriter.State
|
|
49
|
+
emissions:
|
|
50
|
+
probs:
|
|
51
|
+
A: 0.8971401400103951
|
|
52
|
+
C: 0.034286619996534956
|
|
53
|
+
G: 0.034286619996534956
|
|
54
|
+
T: 0.034286619996534956
|
|
55
|
+
track: nukes
|
|
56
|
+
extras:
|
|
57
|
+
ambiguous_char: N
|
|
58
|
+
ambiguous_emission_prob: 0.25
|
|
59
|
+
germline: A
|
|
60
|
+
name: insert_left_A
|
|
61
|
+
transitions:
|
|
62
|
+
IGHD2-8_star_02_0: 0.007130124777183603
|
|
63
|
+
IGHD2-8_star_02_1: 0.007130124777183603
|
|
64
|
+
IGHD2-8_star_02_10: 0.007130124777183603
|
|
65
|
+
IGHD2-8_star_02_11: 0.0064171122994652425
|
|
66
|
+
IGHD2-8_star_02_12: 0.005704099821746882
|
|
67
|
+
IGHD2-8_star_02_13: 0.004991087344028523
|
|
68
|
+
IGHD2-8_star_02_14: 0.004278074866310162
|
|
69
|
+
IGHD2-8_star_02_15: 0.0035650623885918023
|
|
70
|
+
IGHD2-8_star_02_16: 0.0028520499108734424
|
|
71
|
+
IGHD2-8_star_02_17: 0.002139037433155082
|
|
72
|
+
IGHD2-8_star_02_18: 0.0014260249554367216
|
|
73
|
+
IGHD2-8_star_02_19: 0.0007130124777183614
|
|
74
|
+
IGHD2-8_star_02_2: 0.007130124777183603
|
|
75
|
+
IGHD2-8_star_02_20: 9.895035870099437e-19
|
|
76
|
+
IGHD2-8_star_02_21: 0.007130124777183603
|
|
77
|
+
IGHD2-8_star_02_22: 0.007130124777183603
|
|
78
|
+
IGHD2-8_star_02_23: 0.007130124777183603
|
|
79
|
+
IGHD2-8_star_02_24: 0.007130124777183603
|
|
80
|
+
IGHD2-8_star_02_25: 0.007130124777183603
|
|
81
|
+
IGHD2-8_star_02_26: 0.007130124777183603
|
|
82
|
+
IGHD2-8_star_02_27: 0.007130124777183603
|
|
83
|
+
IGHD2-8_star_02_28: 0.007130124777183603
|
|
84
|
+
IGHD2-8_star_02_29: 0.007130124777183603
|
|
85
|
+
IGHD2-8_star_02_3: 0.007130124777183603
|
|
86
|
+
IGHD2-8_star_02_30: 0.007130124777183603
|
|
87
|
+
IGHD2-8_star_02_4: 0.007130124777183603
|
|
88
|
+
IGHD2-8_star_02_5: 0.007130124777183603
|
|
89
|
+
IGHD2-8_star_02_6: 0.007130124777183603
|
|
90
|
+
IGHD2-8_star_02_7: 0.007130124777183603
|
|
91
|
+
IGHD2-8_star_02_8: 0.007130124777183603
|
|
92
|
+
IGHD2-8_star_02_9: 0.007130124777183603
|
|
93
|
+
insert_left_A: 0.1612475116124751
|
|
94
|
+
insert_left_C: 0.27770404777704044
|
|
95
|
+
insert_left_G: 0.17916390179163902
|
|
96
|
+
insert_left_T: 0.20006635700066355
|
|
97
|
+
- !!python/object:python.hmmwriter.State
|
|
98
|
+
emissions:
|
|
99
|
+
probs:
|
|
100
|
+
A: 0.034286619996534956
|
|
101
|
+
C: 0.8971401400103951
|
|
102
|
+
G: 0.034286619996534956
|
|
103
|
+
T: 0.034286619996534956
|
|
104
|
+
track: nukes
|
|
105
|
+
extras:
|
|
106
|
+
ambiguous_char: N
|
|
107
|
+
ambiguous_emission_prob: 0.25
|
|
108
|
+
germline: C
|
|
109
|
+
name: insert_left_C
|
|
110
|
+
transitions:
|
|
111
|
+
IGHD2-8_star_02_0: 0.007130124777183603
|
|
112
|
+
IGHD2-8_star_02_1: 0.007130124777183603
|
|
113
|
+
IGHD2-8_star_02_10: 0.007130124777183603
|
|
114
|
+
IGHD2-8_star_02_11: 0.0064171122994652425
|
|
115
|
+
IGHD2-8_star_02_12: 0.005704099821746882
|
|
116
|
+
IGHD2-8_star_02_13: 0.004991087344028523
|
|
117
|
+
IGHD2-8_star_02_14: 0.004278074866310162
|
|
118
|
+
IGHD2-8_star_02_15: 0.0035650623885918023
|
|
119
|
+
IGHD2-8_star_02_16: 0.0028520499108734424
|
|
120
|
+
IGHD2-8_star_02_17: 0.002139037433155082
|
|
121
|
+
IGHD2-8_star_02_18: 0.0014260249554367216
|
|
122
|
+
IGHD2-8_star_02_19: 0.0007130124777183614
|
|
123
|
+
IGHD2-8_star_02_2: 0.007130124777183603
|
|
124
|
+
IGHD2-8_star_02_20: 9.895035870099437e-19
|
|
125
|
+
IGHD2-8_star_02_21: 0.007130124777183603
|
|
126
|
+
IGHD2-8_star_02_22: 0.007130124777183603
|
|
127
|
+
IGHD2-8_star_02_23: 0.007130124777183603
|
|
128
|
+
IGHD2-8_star_02_24: 0.007130124777183603
|
|
129
|
+
IGHD2-8_star_02_25: 0.007130124777183603
|
|
130
|
+
IGHD2-8_star_02_26: 0.007130124777183603
|
|
131
|
+
IGHD2-8_star_02_27: 0.007130124777183603
|
|
132
|
+
IGHD2-8_star_02_28: 0.007130124777183603
|
|
133
|
+
IGHD2-8_star_02_29: 0.007130124777183603
|
|
134
|
+
IGHD2-8_star_02_3: 0.007130124777183603
|
|
135
|
+
IGHD2-8_star_02_30: 0.007130124777183603
|
|
136
|
+
IGHD2-8_star_02_4: 0.007130124777183603
|
|
137
|
+
IGHD2-8_star_02_5: 0.007130124777183603
|
|
138
|
+
IGHD2-8_star_02_6: 0.007130124777183603
|
|
139
|
+
IGHD2-8_star_02_7: 0.007130124777183603
|
|
140
|
+
IGHD2-8_star_02_8: 0.007130124777183603
|
|
141
|
+
IGHD2-8_star_02_9: 0.007130124777183603
|
|
142
|
+
insert_left_A: 0.1612475116124751
|
|
143
|
+
insert_left_C: 0.27770404777704044
|
|
144
|
+
insert_left_G: 0.17916390179163902
|
|
145
|
+
insert_left_T: 0.20006635700066355
|
|
146
|
+
- !!python/object:python.hmmwriter.State
|
|
147
|
+
emissions:
|
|
148
|
+
probs:
|
|
149
|
+
A: 0.034286619996534956
|
|
150
|
+
C: 0.034286619996534956
|
|
151
|
+
G: 0.8971401400103951
|
|
152
|
+
T: 0.034286619996534956
|
|
153
|
+
track: nukes
|
|
154
|
+
extras:
|
|
155
|
+
ambiguous_char: N
|
|
156
|
+
ambiguous_emission_prob: 0.25
|
|
157
|
+
germline: G
|
|
158
|
+
name: insert_left_G
|
|
159
|
+
transitions:
|
|
160
|
+
IGHD2-8_star_02_0: 0.007130124777183603
|
|
161
|
+
IGHD2-8_star_02_1: 0.007130124777183603
|
|
162
|
+
IGHD2-8_star_02_10: 0.007130124777183603
|
|
163
|
+
IGHD2-8_star_02_11: 0.0064171122994652425
|
|
164
|
+
IGHD2-8_star_02_12: 0.005704099821746882
|
|
165
|
+
IGHD2-8_star_02_13: 0.004991087344028523
|
|
166
|
+
IGHD2-8_star_02_14: 0.004278074866310162
|
|
167
|
+
IGHD2-8_star_02_15: 0.0035650623885918023
|
|
168
|
+
IGHD2-8_star_02_16: 0.0028520499108734424
|
|
169
|
+
IGHD2-8_star_02_17: 0.002139037433155082
|
|
170
|
+
IGHD2-8_star_02_18: 0.0014260249554367216
|
|
171
|
+
IGHD2-8_star_02_19: 0.0007130124777183614
|
|
172
|
+
IGHD2-8_star_02_2: 0.007130124777183603
|
|
173
|
+
IGHD2-8_star_02_20: 9.895035870099437e-19
|
|
174
|
+
IGHD2-8_star_02_21: 0.007130124777183603
|
|
175
|
+
IGHD2-8_star_02_22: 0.007130124777183603
|
|
176
|
+
IGHD2-8_star_02_23: 0.007130124777183603
|
|
177
|
+
IGHD2-8_star_02_24: 0.007130124777183603
|
|
178
|
+
IGHD2-8_star_02_25: 0.007130124777183603
|
|
179
|
+
IGHD2-8_star_02_26: 0.007130124777183603
|
|
180
|
+
IGHD2-8_star_02_27: 0.007130124777183603
|
|
181
|
+
IGHD2-8_star_02_28: 0.007130124777183603
|
|
182
|
+
IGHD2-8_star_02_29: 0.007130124777183603
|
|
183
|
+
IGHD2-8_star_02_3: 0.007130124777183603
|
|
184
|
+
IGHD2-8_star_02_30: 0.007130124777183603
|
|
185
|
+
IGHD2-8_star_02_4: 0.007130124777183603
|
|
186
|
+
IGHD2-8_star_02_5: 0.007130124777183603
|
|
187
|
+
IGHD2-8_star_02_6: 0.007130124777183603
|
|
188
|
+
IGHD2-8_star_02_7: 0.007130124777183603
|
|
189
|
+
IGHD2-8_star_02_8: 0.007130124777183603
|
|
190
|
+
IGHD2-8_star_02_9: 0.007130124777183603
|
|
191
|
+
insert_left_A: 0.1612475116124751
|
|
192
|
+
insert_left_C: 0.27770404777704044
|
|
193
|
+
insert_left_G: 0.17916390179163902
|
|
194
|
+
insert_left_T: 0.20006635700066355
|
|
195
|
+
- !!python/object:python.hmmwriter.State
|
|
196
|
+
emissions:
|
|
197
|
+
probs:
|
|
198
|
+
A: 0.034286619996534956
|
|
199
|
+
C: 0.034286619996534956
|
|
200
|
+
G: 0.034286619996534956
|
|
201
|
+
T: 0.8971401400103951
|
|
202
|
+
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
|
+
IGHD2-8_star_02_0: 0.007130124777183603
|
|
210
|
+
IGHD2-8_star_02_1: 0.007130124777183603
|
|
211
|
+
IGHD2-8_star_02_10: 0.007130124777183603
|
|
212
|
+
IGHD2-8_star_02_11: 0.0064171122994652425
|
|
213
|
+
IGHD2-8_star_02_12: 0.005704099821746882
|
|
214
|
+
IGHD2-8_star_02_13: 0.004991087344028523
|
|
215
|
+
IGHD2-8_star_02_14: 0.004278074866310162
|
|
216
|
+
IGHD2-8_star_02_15: 0.0035650623885918023
|
|
217
|
+
IGHD2-8_star_02_16: 0.0028520499108734424
|
|
218
|
+
IGHD2-8_star_02_17: 0.002139037433155082
|
|
219
|
+
IGHD2-8_star_02_18: 0.0014260249554367216
|
|
220
|
+
IGHD2-8_star_02_19: 0.0007130124777183614
|
|
221
|
+
IGHD2-8_star_02_2: 0.007130124777183603
|
|
222
|
+
IGHD2-8_star_02_20: 9.895035870099437e-19
|
|
223
|
+
IGHD2-8_star_02_21: 0.007130124777183603
|
|
224
|
+
IGHD2-8_star_02_22: 0.007130124777183603
|
|
225
|
+
IGHD2-8_star_02_23: 0.007130124777183603
|
|
226
|
+
IGHD2-8_star_02_24: 0.007130124777183603
|
|
227
|
+
IGHD2-8_star_02_25: 0.007130124777183603
|
|
228
|
+
IGHD2-8_star_02_26: 0.007130124777183603
|
|
229
|
+
IGHD2-8_star_02_27: 0.007130124777183603
|
|
230
|
+
IGHD2-8_star_02_28: 0.007130124777183603
|
|
231
|
+
IGHD2-8_star_02_29: 0.007130124777183603
|
|
232
|
+
IGHD2-8_star_02_3: 0.007130124777183603
|
|
233
|
+
IGHD2-8_star_02_30: 0.007130124777183603
|
|
234
|
+
IGHD2-8_star_02_4: 0.007130124777183603
|
|
235
|
+
IGHD2-8_star_02_5: 0.007130124777183603
|
|
236
|
+
IGHD2-8_star_02_6: 0.007130124777183603
|
|
237
|
+
IGHD2-8_star_02_7: 0.007130124777183603
|
|
238
|
+
IGHD2-8_star_02_8: 0.007130124777183603
|
|
239
|
+
IGHD2-8_star_02_9: 0.007130124777183603
|
|
240
|
+
insert_left_A: 0.1612475116124751
|
|
241
|
+
insert_left_C: 0.27770404777704044
|
|
242
|
+
insert_left_G: 0.17916390179163902
|
|
243
|
+
insert_left_T: 0.20006635700066355
|
|
244
|
+
- !!python/object:python.hmmwriter.State
|
|
245
|
+
emissions:
|
|
246
|
+
probs:
|
|
247
|
+
A: 0.8971401400103951
|
|
248
|
+
C: 0.034286619996534956
|
|
249
|
+
G: 0.034286619996534956
|
|
250
|
+
T: 0.034286619996534956
|
|
251
|
+
track: nukes
|
|
252
|
+
extras:
|
|
253
|
+
ambiguous_char: N
|
|
254
|
+
ambiguous_emission_prob: 0.25
|
|
255
|
+
germline: A
|
|
256
|
+
name: IGHD2-8_star_02_0
|
|
257
|
+
transitions:
|
|
258
|
+
IGHD2-8_star_02_1: 0.9607843137254902
|
|
259
|
+
end: 0.0392156862745098
|
|
260
|
+
- !!python/object:python.hmmwriter.State
|
|
261
|
+
emissions:
|
|
262
|
+
probs:
|
|
263
|
+
A: 0.03418069925617922
|
|
264
|
+
C: 0.03418069925617922
|
|
265
|
+
G: 0.8974579022314624
|
|
266
|
+
T: 0.03418069925617922
|
|
267
|
+
track: nukes
|
|
268
|
+
extras:
|
|
269
|
+
ambiguous_char: N
|
|
270
|
+
ambiguous_emission_prob: 0.25
|
|
271
|
+
germline: G
|
|
272
|
+
name: IGHD2-8_star_02_1
|
|
273
|
+
transitions:
|
|
274
|
+
IGHD2-8_star_02_2: 0.9607843137254902
|
|
275
|
+
end: 0.0392156862745098
|
|
276
|
+
- !!python/object:python.hmmwriter.State
|
|
277
|
+
emissions:
|
|
278
|
+
probs:
|
|
279
|
+
A: 0.03407477851582348
|
|
280
|
+
C: 0.03407477851582348
|
|
281
|
+
G: 0.8977756644525295
|
|
282
|
+
T: 0.03407477851582348
|
|
283
|
+
track: nukes
|
|
284
|
+
extras:
|
|
285
|
+
ambiguous_char: N
|
|
286
|
+
ambiguous_emission_prob: 0.25
|
|
287
|
+
germline: G
|
|
288
|
+
name: IGHD2-8_star_02_2
|
|
289
|
+
transitions:
|
|
290
|
+
IGHD2-8_star_02_3: 0.9607843137254902
|
|
291
|
+
end: 0.0392156862745098
|
|
292
|
+
- !!python/object:python.hmmwriter.State
|
|
293
|
+
emissions:
|
|
294
|
+
probs:
|
|
295
|
+
A: 0.8980934266735967
|
|
296
|
+
C: 0.033968857775467744
|
|
297
|
+
G: 0.033968857775467744
|
|
298
|
+
T: 0.033968857775467744
|
|
299
|
+
track: nukes
|
|
300
|
+
extras:
|
|
301
|
+
ambiguous_char: N
|
|
302
|
+
ambiguous_emission_prob: 0.25
|
|
303
|
+
germline: A
|
|
304
|
+
name: IGHD2-8_star_02_3
|
|
305
|
+
transitions:
|
|
306
|
+
IGHD2-8_star_02_4: 0.9607843137254902
|
|
307
|
+
end: 0.0392156862745098
|
|
308
|
+
- !!python/object:python.hmmwriter.State
|
|
309
|
+
emissions:
|
|
310
|
+
probs:
|
|
311
|
+
A: 0.03386293703511201
|
|
312
|
+
C: 0.03386293703511201
|
|
313
|
+
G: 0.03386293703511201
|
|
314
|
+
T: 0.898411188894664
|
|
315
|
+
track: nukes
|
|
316
|
+
extras:
|
|
317
|
+
ambiguous_char: N
|
|
318
|
+
ambiguous_emission_prob: 0.25
|
|
319
|
+
germline: T
|
|
320
|
+
name: IGHD2-8_star_02_4
|
|
321
|
+
transitions:
|
|
322
|
+
IGHD2-8_star_02_5: 0.9607843137254902
|
|
323
|
+
end: 0.0392156862745098
|
|
324
|
+
- !!python/object:python.hmmwriter.State
|
|
325
|
+
emissions:
|
|
326
|
+
probs:
|
|
327
|
+
A: 0.8987289511157311
|
|
328
|
+
C: 0.033757016294756276
|
|
329
|
+
G: 0.033757016294756276
|
|
330
|
+
T: 0.033757016294756276
|
|
331
|
+
track: nukes
|
|
332
|
+
extras:
|
|
333
|
+
ambiguous_char: N
|
|
334
|
+
ambiguous_emission_prob: 0.25
|
|
335
|
+
germline: A
|
|
336
|
+
name: IGHD2-8_star_02_5
|
|
337
|
+
transitions:
|
|
338
|
+
IGHD2-8_star_02_6: 0.9607843137254902
|
|
339
|
+
end: 0.0392156862745098
|
|
340
|
+
- !!python/object:python.hmmwriter.State
|
|
341
|
+
emissions:
|
|
342
|
+
probs:
|
|
343
|
+
A: 0.033651095554400545
|
|
344
|
+
C: 0.033651095554400545
|
|
345
|
+
G: 0.033651095554400545
|
|
346
|
+
T: 0.8990467133367983
|
|
347
|
+
track: nukes
|
|
348
|
+
extras:
|
|
349
|
+
ambiguous_char: N
|
|
350
|
+
ambiguous_emission_prob: 0.25
|
|
351
|
+
germline: T
|
|
352
|
+
name: IGHD2-8_star_02_6
|
|
353
|
+
transitions:
|
|
354
|
+
IGHD2-8_star_02_7: 0.9607843137254902
|
|
355
|
+
end: 0.0392156862745098
|
|
356
|
+
- !!python/object:python.hmmwriter.State
|
|
357
|
+
emissions:
|
|
358
|
+
probs:
|
|
359
|
+
A: 0.0335451748140448
|
|
360
|
+
C: 0.0335451748140448
|
|
361
|
+
G: 0.0335451748140448
|
|
362
|
+
T: 0.8993644755578656
|
|
363
|
+
track: nukes
|
|
364
|
+
extras:
|
|
365
|
+
ambiguous_char: N
|
|
366
|
+
ambiguous_emission_prob: 0.25
|
|
367
|
+
germline: T
|
|
368
|
+
name: IGHD2-8_star_02_7
|
|
369
|
+
transitions:
|
|
370
|
+
IGHD2-8_star_02_8: 0.9607843137254902
|
|
371
|
+
end: 0.0392156862745098
|
|
372
|
+
- !!python/object:python.hmmwriter.State
|
|
373
|
+
emissions:
|
|
374
|
+
probs:
|
|
375
|
+
A: 0.03343925407368907
|
|
376
|
+
C: 0.03343925407368907
|
|
377
|
+
G: 0.8996822377789327
|
|
378
|
+
T: 0.03343925407368907
|
|
379
|
+
track: nukes
|
|
380
|
+
extras:
|
|
381
|
+
ambiguous_char: N
|
|
382
|
+
ambiguous_emission_prob: 0.25
|
|
383
|
+
germline: G
|
|
384
|
+
name: IGHD2-8_star_02_8
|
|
385
|
+
transitions:
|
|
386
|
+
IGHD2-8_star_02_9: 0.9607843137254902
|
|
387
|
+
end: 0.0392156862745098
|
|
388
|
+
- !!python/object:python.hmmwriter.State
|
|
389
|
+
emissions:
|
|
390
|
+
probs:
|
|
391
|
+
A: 0.03333333333333333
|
|
392
|
+
C: 0.03333333333333333
|
|
393
|
+
G: 0.03333333333333333
|
|
394
|
+
T: 0.9
|
|
395
|
+
track: nukes
|
|
396
|
+
extras:
|
|
397
|
+
ambiguous_char: N
|
|
398
|
+
ambiguous_emission_prob: 0.25
|
|
399
|
+
germline: T
|
|
400
|
+
name: IGHD2-8_star_02_9
|
|
401
|
+
transitions:
|
|
402
|
+
IGHD2-8_star_02_10: 0.9607843137254902
|
|
403
|
+
end: 0.0392156862745098
|
|
404
|
+
- !!python/object:python.hmmwriter.State
|
|
405
|
+
emissions:
|
|
406
|
+
probs:
|
|
407
|
+
A: 0.892384434032225
|
|
408
|
+
C: 0.03587185532259167
|
|
409
|
+
G: 0.03587185532259167
|
|
410
|
+
T: 0.03587185532259167
|
|
411
|
+
track: nukes
|
|
412
|
+
extras:
|
|
413
|
+
ambiguous_char: N
|
|
414
|
+
ambiguous_emission_prob: 0.25
|
|
415
|
+
germline: A
|
|
416
|
+
name: IGHD2-8_star_02_10
|
|
417
|
+
transitions:
|
|
418
|
+
IGHD2-8_star_02_11: 1.0
|
|
419
|
+
- !!python/object:python.hmmwriter.State
|
|
420
|
+
emissions:
|
|
421
|
+
probs:
|
|
422
|
+
A: 0.03587185532259167
|
|
423
|
+
C: 0.892384434032225
|
|
424
|
+
G: 0.03587185532259167
|
|
425
|
+
T: 0.03587185532259167
|
|
426
|
+
track: nukes
|
|
427
|
+
extras:
|
|
428
|
+
ambiguous_char: N
|
|
429
|
+
ambiguous_emission_prob: 0.25
|
|
430
|
+
germline: C
|
|
431
|
+
name: IGHD2-8_star_02_11
|
|
432
|
+
transitions:
|
|
433
|
+
IGHD2-8_star_02_12: 0.996078431372549
|
|
434
|
+
end: 0.003921568627450986
|
|
435
|
+
- !!python/object:python.hmmwriter.State
|
|
436
|
+
emissions:
|
|
437
|
+
probs:
|
|
438
|
+
A: 0.03587185532259167
|
|
439
|
+
C: 0.03587185532259167
|
|
440
|
+
G: 0.03587185532259167
|
|
441
|
+
T: 0.892384434032225
|
|
442
|
+
track: nukes
|
|
443
|
+
extras:
|
|
444
|
+
ambiguous_char: N
|
|
445
|
+
ambiguous_emission_prob: 0.25
|
|
446
|
+
germline: T
|
|
447
|
+
name: IGHD2-8_star_02_12
|
|
448
|
+
transitions:
|
|
449
|
+
IGHD2-8_star_02_13: 0.9921568627450981
|
|
450
|
+
end: 0.007843137254901966
|
|
451
|
+
- !!python/object:python.hmmwriter.State
|
|
452
|
+
emissions:
|
|
453
|
+
probs:
|
|
454
|
+
A: 0.03587185532259167
|
|
455
|
+
C: 0.03587185532259167
|
|
456
|
+
G: 0.892384434032225
|
|
457
|
+
T: 0.03587185532259167
|
|
458
|
+
track: nukes
|
|
459
|
+
extras:
|
|
460
|
+
ambiguous_char: N
|
|
461
|
+
ambiguous_emission_prob: 0.25
|
|
462
|
+
germline: G
|
|
463
|
+
name: IGHD2-8_star_02_13
|
|
464
|
+
transitions:
|
|
465
|
+
IGHD2-8_star_02_14: 0.9882352941176471
|
|
466
|
+
end: 0.011764705882352948
|
|
467
|
+
- !!python/object:python.hmmwriter.State
|
|
468
|
+
emissions:
|
|
469
|
+
probs:
|
|
470
|
+
A: 0.03587185532259167
|
|
471
|
+
C: 0.03587185532259167
|
|
472
|
+
G: 0.892384434032225
|
|
473
|
+
T: 0.03587185532259167
|
|
474
|
+
track: nukes
|
|
475
|
+
extras:
|
|
476
|
+
ambiguous_char: N
|
|
477
|
+
ambiguous_emission_prob: 0.25
|
|
478
|
+
germline: G
|
|
479
|
+
name: IGHD2-8_star_02_14
|
|
480
|
+
transitions:
|
|
481
|
+
IGHD2-8_star_02_15: 0.984313725490196
|
|
482
|
+
end: 0.01568627450980393
|
|
483
|
+
- !!python/object:python.hmmwriter.State
|
|
484
|
+
emissions:
|
|
485
|
+
probs:
|
|
486
|
+
A: 0.03587185532259167
|
|
487
|
+
C: 0.03587185532259167
|
|
488
|
+
G: 0.03587185532259167
|
|
489
|
+
T: 0.892384434032225
|
|
490
|
+
track: nukes
|
|
491
|
+
extras:
|
|
492
|
+
ambiguous_char: N
|
|
493
|
+
ambiguous_emission_prob: 0.25
|
|
494
|
+
germline: T
|
|
495
|
+
name: IGHD2-8_star_02_15
|
|
496
|
+
transitions:
|
|
497
|
+
IGHD2-8_star_02_16: 0.9803921568627451
|
|
498
|
+
end: 0.019607843137254905
|
|
499
|
+
- !!python/object:python.hmmwriter.State
|
|
500
|
+
emissions:
|
|
501
|
+
probs:
|
|
502
|
+
A: 0.03587185532259167
|
|
503
|
+
C: 0.03587185532259167
|
|
504
|
+
G: 0.892384434032225
|
|
505
|
+
T: 0.03587185532259167
|
|
506
|
+
track: nukes
|
|
507
|
+
extras:
|
|
508
|
+
ambiguous_char: N
|
|
509
|
+
ambiguous_emission_prob: 0.25
|
|
510
|
+
germline: G
|
|
511
|
+
name: IGHD2-8_star_02_16
|
|
512
|
+
transitions:
|
|
513
|
+
IGHD2-8_star_02_17: 0.9764705882352941
|
|
514
|
+
end: 0.023529411764705885
|
|
515
|
+
- !!python/object:python.hmmwriter.State
|
|
516
|
+
emissions:
|
|
517
|
+
probs:
|
|
518
|
+
A: 0.03587185532259167
|
|
519
|
+
C: 0.03587185532259167
|
|
520
|
+
G: 0.892384434032225
|
|
521
|
+
T: 0.03587185532259167
|
|
522
|
+
track: nukes
|
|
523
|
+
extras:
|
|
524
|
+
ambiguous_char: N
|
|
525
|
+
ambiguous_emission_prob: 0.25
|
|
526
|
+
germline: G
|
|
527
|
+
name: IGHD2-8_star_02_17
|
|
528
|
+
transitions:
|
|
529
|
+
IGHD2-8_star_02_18: 0.9725490196078431
|
|
530
|
+
end: 0.027450980392156866
|
|
531
|
+
- !!python/object:python.hmmwriter.State
|
|
532
|
+
emissions:
|
|
533
|
+
probs:
|
|
534
|
+
A: 0.0375
|
|
535
|
+
C: 0.0375
|
|
536
|
+
G: 0.0375
|
|
537
|
+
T: 0.8875
|
|
538
|
+
track: nukes
|
|
539
|
+
extras:
|
|
540
|
+
ambiguous_char: N
|
|
541
|
+
ambiguous_emission_prob: 0.25
|
|
542
|
+
germline: T
|
|
543
|
+
name: IGHD2-8_star_02_18
|
|
544
|
+
transitions:
|
|
545
|
+
IGHD2-8_star_02_19: 0.9686274509803922
|
|
546
|
+
end: 0.03137254901960784
|
|
547
|
+
- !!python/object:python.hmmwriter.State
|
|
548
|
+
emissions:
|
|
549
|
+
probs:
|
|
550
|
+
A: 0.03587185532259167
|
|
551
|
+
C: 0.03587185532259167
|
|
552
|
+
G: 0.892384434032225
|
|
553
|
+
T: 0.03587185532259167
|
|
554
|
+
track: nukes
|
|
555
|
+
extras:
|
|
556
|
+
ambiguous_char: N
|
|
557
|
+
ambiguous_emission_prob: 0.25
|
|
558
|
+
germline: G
|
|
559
|
+
name: IGHD2-8_star_02_19
|
|
560
|
+
transitions:
|
|
561
|
+
IGHD2-8_star_02_20: 0.9647058823529412
|
|
562
|
+
end: 0.03529411764705882
|
|
563
|
+
- !!python/object:python.hmmwriter.State
|
|
564
|
+
emissions:
|
|
565
|
+
probs:
|
|
566
|
+
A: 0.03587185532259167
|
|
567
|
+
C: 0.03587185532259167
|
|
568
|
+
G: 0.03587185532259167
|
|
569
|
+
T: 0.892384434032225
|
|
570
|
+
track: nukes
|
|
571
|
+
extras:
|
|
572
|
+
ambiguous_char: N
|
|
573
|
+
ambiguous_emission_prob: 0.25
|
|
574
|
+
germline: T
|
|
575
|
+
name: IGHD2-8_star_02_20
|
|
576
|
+
transitions:
|
|
577
|
+
IGHD2-8_star_02_21: 0.9607843137254902
|
|
578
|
+
end: 0.0392156862745098
|
|
579
|
+
- !!python/object:python.hmmwriter.State
|
|
580
|
+
emissions:
|
|
581
|
+
probs:
|
|
582
|
+
A: 0.9
|
|
583
|
+
C: 0.03333333333333333
|
|
584
|
+
G: 0.03333333333333333
|
|
585
|
+
T: 0.03333333333333333
|
|
586
|
+
track: nukes
|
|
587
|
+
extras:
|
|
588
|
+
ambiguous_char: N
|
|
589
|
+
ambiguous_emission_prob: 0.25
|
|
590
|
+
germline: A
|
|
591
|
+
name: IGHD2-8_star_02_21
|
|
592
|
+
transitions:
|
|
593
|
+
IGHD2-8_star_02_22: 0.9607843137254902
|
|
594
|
+
end: 0.0392156862745098
|
|
595
|
+
- !!python/object:python.hmmwriter.State
|
|
596
|
+
emissions:
|
|
597
|
+
probs:
|
|
598
|
+
A: 0.03343925407368907
|
|
599
|
+
C: 0.03343925407368907
|
|
600
|
+
G: 0.03343925407368907
|
|
601
|
+
T: 0.8996822377789327
|
|
602
|
+
track: nukes
|
|
603
|
+
extras:
|
|
604
|
+
ambiguous_char: N
|
|
605
|
+
ambiguous_emission_prob: 0.25
|
|
606
|
+
germline: T
|
|
607
|
+
name: IGHD2-8_star_02_22
|
|
608
|
+
transitions:
|
|
609
|
+
IGHD2-8_star_02_23: 0.9607843137254902
|
|
610
|
+
end: 0.0392156862745098
|
|
611
|
+
- !!python/object:python.hmmwriter.State
|
|
612
|
+
emissions:
|
|
613
|
+
probs:
|
|
614
|
+
A: 0.0335451748140448
|
|
615
|
+
C: 0.0335451748140448
|
|
616
|
+
G: 0.8993644755578656
|
|
617
|
+
T: 0.0335451748140448
|
|
618
|
+
track: nukes
|
|
619
|
+
extras:
|
|
620
|
+
ambiguous_char: N
|
|
621
|
+
ambiguous_emission_prob: 0.25
|
|
622
|
+
germline: G
|
|
623
|
+
name: IGHD2-8_star_02_23
|
|
624
|
+
transitions:
|
|
625
|
+
IGHD2-8_star_02_24: 0.9607843137254902
|
|
626
|
+
end: 0.0392156862745098
|
|
627
|
+
- !!python/object:python.hmmwriter.State
|
|
628
|
+
emissions:
|
|
629
|
+
probs:
|
|
630
|
+
A: 0.033651095554400545
|
|
631
|
+
C: 0.8990467133367983
|
|
632
|
+
G: 0.033651095554400545
|
|
633
|
+
T: 0.033651095554400545
|
|
634
|
+
track: nukes
|
|
635
|
+
extras:
|
|
636
|
+
ambiguous_char: N
|
|
637
|
+
ambiguous_emission_prob: 0.25
|
|
638
|
+
germline: C
|
|
639
|
+
name: IGHD2-8_star_02_24
|
|
640
|
+
transitions:
|
|
641
|
+
IGHD2-8_star_02_25: 0.9607843137254902
|
|
642
|
+
end: 0.0392156862745098
|
|
643
|
+
- !!python/object:python.hmmwriter.State
|
|
644
|
+
emissions:
|
|
645
|
+
probs:
|
|
646
|
+
A: 0.033757016294756276
|
|
647
|
+
C: 0.033757016294756276
|
|
648
|
+
G: 0.033757016294756276
|
|
649
|
+
T: 0.8987289511157311
|
|
650
|
+
track: nukes
|
|
651
|
+
extras:
|
|
652
|
+
ambiguous_char: N
|
|
653
|
+
ambiguous_emission_prob: 0.25
|
|
654
|
+
germline: T
|
|
655
|
+
name: IGHD2-8_star_02_25
|
|
656
|
+
transitions:
|
|
657
|
+
IGHD2-8_star_02_26: 0.9607843137254902
|
|
658
|
+
end: 0.0392156862745098
|
|
659
|
+
- !!python/object:python.hmmwriter.State
|
|
660
|
+
emissions:
|
|
661
|
+
probs:
|
|
662
|
+
A: 0.898411188894664
|
|
663
|
+
C: 0.03386293703511201
|
|
664
|
+
G: 0.03386293703511201
|
|
665
|
+
T: 0.03386293703511201
|
|
666
|
+
track: nukes
|
|
667
|
+
extras:
|
|
668
|
+
ambiguous_char: N
|
|
669
|
+
ambiguous_emission_prob: 0.25
|
|
670
|
+
germline: A
|
|
671
|
+
name: IGHD2-8_star_02_26
|
|
672
|
+
transitions:
|
|
673
|
+
IGHD2-8_star_02_27: 0.9607843137254902
|
|
674
|
+
end: 0.0392156862745098
|
|
675
|
+
- !!python/object:python.hmmwriter.State
|
|
676
|
+
emissions:
|
|
677
|
+
probs:
|
|
678
|
+
A: 0.033968857775467744
|
|
679
|
+
C: 0.033968857775467744
|
|
680
|
+
G: 0.033968857775467744
|
|
681
|
+
T: 0.8980934266735967
|
|
682
|
+
track: nukes
|
|
683
|
+
extras:
|
|
684
|
+
ambiguous_char: N
|
|
685
|
+
ambiguous_emission_prob: 0.25
|
|
686
|
+
germline: T
|
|
687
|
+
name: IGHD2-8_star_02_27
|
|
688
|
+
transitions:
|
|
689
|
+
IGHD2-8_star_02_28: 0.9607843137254902
|
|
690
|
+
end: 0.0392156862745098
|
|
691
|
+
- !!python/object:python.hmmwriter.State
|
|
692
|
+
emissions:
|
|
693
|
+
probs:
|
|
694
|
+
A: 0.8977756644525295
|
|
695
|
+
C: 0.03407477851582348
|
|
696
|
+
G: 0.03407477851582348
|
|
697
|
+
T: 0.03407477851582348
|
|
698
|
+
track: nukes
|
|
699
|
+
extras:
|
|
700
|
+
ambiguous_char: N
|
|
701
|
+
ambiguous_emission_prob: 0.25
|
|
702
|
+
germline: A
|
|
703
|
+
name: IGHD2-8_star_02_28
|
|
704
|
+
transitions:
|
|
705
|
+
IGHD2-8_star_02_29: 0.9607843137254902
|
|
706
|
+
end: 0.0392156862745098
|
|
707
|
+
- !!python/object:python.hmmwriter.State
|
|
708
|
+
emissions:
|
|
709
|
+
probs:
|
|
710
|
+
A: 0.03418069925617922
|
|
711
|
+
C: 0.8974579022314624
|
|
712
|
+
G: 0.03418069925617922
|
|
713
|
+
T: 0.03418069925617922
|
|
714
|
+
track: nukes
|
|
715
|
+
extras:
|
|
716
|
+
ambiguous_char: N
|
|
717
|
+
ambiguous_emission_prob: 0.25
|
|
718
|
+
germline: C
|
|
719
|
+
name: IGHD2-8_star_02_29
|
|
720
|
+
transitions:
|
|
721
|
+
IGHD2-8_star_02_30: 0.9607843137254902
|
|
722
|
+
end: 0.0392156862745098
|
|
723
|
+
- !!python/object:python.hmmwriter.State
|
|
724
|
+
emissions:
|
|
725
|
+
probs:
|
|
726
|
+
A: 0.034286619996534956
|
|
727
|
+
C: 0.8971401400103951
|
|
728
|
+
G: 0.034286619996534956
|
|
729
|
+
T: 0.034286619996534956
|
|
730
|
+
track: nukes
|
|
731
|
+
extras:
|
|
732
|
+
ambiguous_char: N
|
|
733
|
+
ambiguous_emission_prob: 0.25
|
|
734
|
+
germline: C
|
|
735
|
+
name: IGHD2-8_star_02_30
|
|
736
|
+
transitions:
|
|
737
|
+
end: 1.0
|
|
738
|
+
tracks:
|
|
739
|
+
nukes:
|
|
740
|
+
- A
|
|
741
|
+
- C
|
|
742
|
+
- G
|
|
743
|
+
- T
|