partis-bcr 1.0.11.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.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.dev3.data}/scripts/partis-test.py +6 -0
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/METADATA +1 -1
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/RECORD +652 -125
- 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 +10 -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
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- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-germlines.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/gctree-run.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/parse-output.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/split-loci.py +0 -0
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/WHEEL +0 -0
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/entry_points.txt +0 -0
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overall_mute_freq: 0.08760869565217394
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per_gene_mute_freq: 0.10335118682623552
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IGHD3-10_star_03_1: 0.018518518518518517
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IGHD3-10_star_03_10: 0.016460905349794237
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IGHD3-10_star_03_11: 0.014403292181069957
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IGHD3-10_star_03_12: 0.012345679012345677
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IGHD3-10_star_03_13: 0.010288065843621396
|
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|
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|
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|
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|
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IGHD3-10_star_03_17: 0.0020576131687242765
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|
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|
+
IGHD3-10_star_03_18: 0.018518518518518517
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|
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|
+
IGHD3-10_star_03_19: 0.018518518518518517
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|
25
|
+
IGHD3-10_star_03_2: 0.018518518518518517
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|
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|
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|
28
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+
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|
29
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|
30
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IGHD3-10_star_03_28: 0.018518518518518517
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|
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|
36
|
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IGHD3-10_star_03_3: 0.018518518518518517
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|
37
|
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IGHD3-10_star_03_30: 0.018518518518518517
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|
38
|
+
IGHD3-10_star_03_4: 0.018518518518518517
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|
39
|
+
IGHD3-10_star_03_5: 0.018518518518518517
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|
40
|
+
IGHD3-10_star_03_6: 0.018518518518518517
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|
41
|
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IGHD3-10_star_03_7: 0.018518518518518517
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|
42
|
+
IGHD3-10_star_03_8: 0.018518518518518517
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|
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|
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IGHD3-10_star_03_9: 0.018518518518518517
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|
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|
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|
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insert_left_T: 0.12030075187969924
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|
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|
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- !!python/object:python.hmmwriter.State
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|
49
|
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emissions:
|
|
50
|
+
probs:
|
|
51
|
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A: 0.8966488131737644
|
|
52
|
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C: 0.034450395608745174
|
|
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G: 0.034450395608745174
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|
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|
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T: 0.034450395608745174
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|
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|
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track: nukes
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|
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|
+
extras:
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|
57
|
+
ambiguous_char: N
|
|
58
|
+
ambiguous_emission_prob: 0.25
|
|
59
|
+
germline: A
|
|
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|
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name: insert_left_A
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|
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transitions:
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|
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|
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IGHD3-10_star_03_1: 0.004938271604938271
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IGHD3-10_star_03_10: 0.004389574759945129
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IGHD3-10_star_03_11: 0.003840877914951988
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IGHD3-10_star_03_12: 0.0032921810699588464
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IGHD3-10_star_03_13: 0.002743484224965705
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IGHD3-10_star_03_14: 0.002194787379972564
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IGHD3-10_star_03_17: 0.0005486968449931403
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IGHD3-10_star_03_18: 0.004938271604938271
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|
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IGHD3-10_star_03_19: 0.004938271604938271
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|
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|
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IGHD3-10_star_03_2: 0.004938271604938271
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|
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IGHD3-10_star_03_21: 0.004938271604938271
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IGHD3-10_star_03_22: 0.004938271604938271
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|
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IGHD3-10_star_03_23: 0.004938271604938271
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IGHD3-10_star_03_24: 0.004938271604938271
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|
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IGHD3-10_star_03_25: 0.004938271604938271
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|
81
|
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IGHD3-10_star_03_26: 0.004938271604938271
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|
82
|
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IGHD3-10_star_03_27: 0.004938271604938271
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|
83
|
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IGHD3-10_star_03_28: 0.004938271604938271
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|
84
|
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IGHD3-10_star_03_29: 0.004938271604938271
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|
85
|
+
IGHD3-10_star_03_3: 0.004938271604938271
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|
86
|
+
IGHD3-10_star_03_30: 0.004938271604938271
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|
87
|
+
IGHD3-10_star_03_4: 0.004938271604938271
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|
88
|
+
IGHD3-10_star_03_5: 0.004938271604938271
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|
89
|
+
IGHD3-10_star_03_6: 0.004938271604938271
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|
90
|
+
IGHD3-10_star_03_7: 0.004938271604938271
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|
91
|
+
IGHD3-10_star_03_8: 0.004938271604938271
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|
92
|
+
IGHD3-10_star_03_9: 0.004938271604938271
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|
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|
+
insert_left_A: 0.16290726817042606
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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_T: 0.20852130325814536
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|
97
|
+
- !!python/object:python.hmmwriter.State
|
|
98
|
+
emissions:
|
|
99
|
+
probs:
|
|
100
|
+
A: 0.034450395608745174
|
|
101
|
+
C: 0.8966488131737644
|
|
102
|
+
G: 0.034450395608745174
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|
103
|
+
T: 0.034450395608745174
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|
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
|
+
IGHD3-10_star_03_0: 0.004938271604938271
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|
112
|
+
IGHD3-10_star_03_1: 0.004938271604938271
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|
113
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IGHD3-10_star_03_10: 0.004389574759945129
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|
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IGHD3-10_star_03_11: 0.003840877914951988
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|
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|
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IGHD3-10_star_03_12: 0.0032921810699588464
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|
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IGHD3-10_star_03_13: 0.002743484224965705
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IGHD3-10_star_03_14: 0.002194787379972564
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|
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IGHD3-10_star_03_15: 0.0016460905349794225
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IGHD3-10_star_03_16: 0.0010973936899862815
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|
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|
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IGHD3-10_star_03_17: 0.0005486968449931403
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|
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|
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IGHD3-10_star_03_18: 0.004938271604938271
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|
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|
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IGHD3-10_star_03_19: 0.004938271604938271
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|
123
|
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IGHD3-10_star_03_2: 0.004938271604938271
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|
124
|
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IGHD3-10_star_03_20: 0.004938271604938271
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|
125
|
+
IGHD3-10_star_03_21: 0.004938271604938271
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|
126
|
+
IGHD3-10_star_03_22: 0.004938271604938271
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|
127
|
+
IGHD3-10_star_03_23: 0.004938271604938271
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|
128
|
+
IGHD3-10_star_03_24: 0.004938271604938271
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|
129
|
+
IGHD3-10_star_03_25: 0.004938271604938271
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|
130
|
+
IGHD3-10_star_03_26: 0.004938271604938271
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|
131
|
+
IGHD3-10_star_03_27: 0.004938271604938271
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|
132
|
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IGHD3-10_star_03_28: 0.004938271604938271
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|
133
|
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IGHD3-10_star_03_29: 0.004938271604938271
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|
134
|
+
IGHD3-10_star_03_3: 0.004938271604938271
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|
135
|
+
IGHD3-10_star_03_30: 0.004938271604938271
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|
136
|
+
IGHD3-10_star_03_4: 0.004938271604938271
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|
137
|
+
IGHD3-10_star_03_5: 0.004938271604938271
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|
138
|
+
IGHD3-10_star_03_6: 0.004938271604938271
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|
139
|
+
IGHD3-10_star_03_7: 0.004938271604938271
|
|
140
|
+
IGHD3-10_star_03_8: 0.004938271604938271
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|
141
|
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IGHD3-10_star_03_9: 0.004938271604938271
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|
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|
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insert_left_A: 0.16290726817042606
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|
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|
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insert_left_C: 0.2932330827067669
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|
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|
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insert_left_G: 0.20200501253132833
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|
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|
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insert_left_T: 0.20852130325814536
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|
146
|
+
- !!python/object:python.hmmwriter.State
|
|
147
|
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emissions:
|
|
148
|
+
probs:
|
|
149
|
+
A: 0.034450395608745174
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|
150
|
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C: 0.034450395608745174
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|
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|
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G: 0.8966488131737644
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|
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|
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T: 0.034450395608745174
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|
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|
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track: nukes
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|
154
|
+
extras:
|
|
155
|
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ambiguous_char: N
|
|
156
|
+
ambiguous_emission_prob: 0.25
|
|
157
|
+
germline: G
|
|
158
|
+
name: insert_left_G
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|
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|
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transitions:
|
|
160
|
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IGHD3-10_star_03_0: 0.004938271604938271
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|
161
|
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IGHD3-10_star_03_1: 0.004938271604938271
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|
162
|
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IGHD3-10_star_03_10: 0.004389574759945129
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|
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|
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IGHD3-10_star_03_11: 0.003840877914951988
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IGHD3-10_star_03_12: 0.0032921810699588464
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IGHD3-10_star_03_13: 0.002743484224965705
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IGHD3-10_star_03_14: 0.002194787379972564
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|
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IGHD3-10_star_03_16: 0.0010973936899862815
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|
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|
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IGHD3-10_star_03_17: 0.0005486968449931403
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|
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|
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IGHD3-10_star_03_18: 0.004938271604938271
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|
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|
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IGHD3-10_star_03_19: 0.004938271604938271
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|
172
|
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IGHD3-10_star_03_2: 0.004938271604938271
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|
173
|
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IGHD3-10_star_03_20: 0.004938271604938271
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|
174
|
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IGHD3-10_star_03_21: 0.004938271604938271
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|
175
|
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IGHD3-10_star_03_22: 0.004938271604938271
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|
176
|
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IGHD3-10_star_03_23: 0.004938271604938271
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|
177
|
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IGHD3-10_star_03_24: 0.004938271604938271
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|
178
|
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IGHD3-10_star_03_25: 0.004938271604938271
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|
179
|
+
IGHD3-10_star_03_26: 0.004938271604938271
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|
180
|
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IGHD3-10_star_03_27: 0.004938271604938271
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|
181
|
+
IGHD3-10_star_03_28: 0.004938271604938271
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|
182
|
+
IGHD3-10_star_03_29: 0.004938271604938271
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|
183
|
+
IGHD3-10_star_03_3: 0.004938271604938271
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|
184
|
+
IGHD3-10_star_03_30: 0.004938271604938271
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|
185
|
+
IGHD3-10_star_03_4: 0.004938271604938271
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|
186
|
+
IGHD3-10_star_03_5: 0.004938271604938271
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|
187
|
+
IGHD3-10_star_03_6: 0.004938271604938271
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|
188
|
+
IGHD3-10_star_03_7: 0.004938271604938271
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|
189
|
+
IGHD3-10_star_03_8: 0.004938271604938271
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|
190
|
+
IGHD3-10_star_03_9: 0.004938271604938271
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|
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|
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insert_left_A: 0.16290726817042606
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|
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|
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insert_left_C: 0.2932330827067669
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|
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|
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insert_left_G: 0.20200501253132833
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|
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|
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insert_left_T: 0.20852130325814536
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|
195
|
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- !!python/object:python.hmmwriter.State
|
|
196
|
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emissions:
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|
197
|
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probs:
|
|
198
|
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A: 0.034450395608745174
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|
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C: 0.034450395608745174
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|
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|
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G: 0.034450395608745174
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|
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T: 0.8966488131737644
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|
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|
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track: nukes
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|
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|
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extras:
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|
204
|
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ambiguous_char: N
|
|
205
|
+
ambiguous_emission_prob: 0.25
|
|
206
|
+
germline: T
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|
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|
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name: insert_left_T
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|
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|
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transitions:
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|
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|
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IGHD3-10_star_03_0: 0.004938271604938271
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|
210
|
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IGHD3-10_star_03_1: 0.004938271604938271
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|
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|
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IGHD3-10_star_03_10: 0.004389574759945129
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|
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IGHD3-10_star_03_11: 0.003840877914951988
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IGHD3-10_star_03_12: 0.0032921810699588464
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IGHD3-10_star_03_16: 0.0010973936899862815
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IGHD3-10_star_03_17: 0.0005486968449931403
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|
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|
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IGHD3-10_star_03_18: 0.004938271604938271
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|
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|
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IGHD3-10_star_03_19: 0.004938271604938271
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|
221
|
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IGHD3-10_star_03_2: 0.004938271604938271
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|
222
|
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IGHD3-10_star_03_20: 0.004938271604938271
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|
223
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IGHD3-10_star_03_21: 0.004938271604938271
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|
224
|
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IGHD3-10_star_03_22: 0.004938271604938271
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|
225
|
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IGHD3-10_star_03_23: 0.004938271604938271
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|
226
|
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IGHD3-10_star_03_24: 0.004938271604938271
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|
227
|
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IGHD3-10_star_03_25: 0.004938271604938271
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|
228
|
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IGHD3-10_star_03_26: 0.004938271604938271
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|
229
|
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IGHD3-10_star_03_27: 0.004938271604938271
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|
230
|
+
IGHD3-10_star_03_28: 0.004938271604938271
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|
231
|
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IGHD3-10_star_03_29: 0.004938271604938271
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|
232
|
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IGHD3-10_star_03_3: 0.004938271604938271
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|
233
|
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IGHD3-10_star_03_30: 0.004938271604938271
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|
234
|
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IGHD3-10_star_03_4: 0.004938271604938271
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|
235
|
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IGHD3-10_star_03_5: 0.004938271604938271
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|
236
|
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IGHD3-10_star_03_6: 0.004938271604938271
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|
237
|
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IGHD3-10_star_03_7: 0.004938271604938271
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|
238
|
+
IGHD3-10_star_03_8: 0.004938271604938271
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|
239
|
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IGHD3-10_star_03_9: 0.004938271604938271
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|
240
|
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insert_left_A: 0.16290726817042606
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|
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|
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insert_left_C: 0.2932330827067669
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|
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|
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insert_left_G: 0.20200501253132833
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|
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|
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insert_left_T: 0.20852130325814536
|
|
244
|
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- !!python/object:python.hmmwriter.State
|
|
245
|
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emissions:
|
|
246
|
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probs:
|
|
247
|
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A: 0.034450395608745174
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|
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|
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C: 0.034450395608745174
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|
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|
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G: 0.8966488131737644
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|
250
|
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T: 0.034450395608745174
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|
251
|
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track: nukes
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|
252
|
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extras:
|
|
253
|
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ambiguous_char: N
|
|
254
|
+
ambiguous_emission_prob: 0.25
|
|
255
|
+
germline: G
|
|
256
|
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name: IGHD3-10_star_03_0
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|
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|
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transitions:
|
|
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|
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IGHD3-10_star_03_1: 0.962962962962963
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|
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