partis-bcr 1.0.11__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.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/partis-test.py +6 -0
- {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/METADATA +1 -1
- {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/RECORD +655 -128
- 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.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-alleles.py +0 -0
- {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-germlines.py +0 -0
- {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
- {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
- {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/gctree-run.py +0 -0
- {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
- {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/parse-output.py +0 -0
- {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/split-loci.py +0 -0
- {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/WHEEL +0 -0
- {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/entry_points.txt +0 -0
- {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/licenses/COPYING +0 -0
- {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/top_level.txt +0 -0
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18
|
+
IGHD2-21_star_01_13: 0.002902757619738752
|
|
19
|
+
IGHD2-21_star_01_14: 0.002902757619738752
|
|
20
|
+
IGHD2-21_star_01_15: 0.002902757619738752
|
|
21
|
+
IGHD2-21_star_01_16: 0.002902757619738752
|
|
22
|
+
IGHD2-21_star_01_17: 0.002902757619738752
|
|
23
|
+
IGHD2-21_star_01_18: 0.002902757619738752
|
|
24
|
+
IGHD2-21_star_01_19: 0.002902757619738752
|
|
25
|
+
IGHD2-21_star_01_2: 0.002902757619738752
|
|
26
|
+
IGHD2-21_star_01_20: 0.002902757619738752
|
|
27
|
+
IGHD2-21_star_01_21: 0.002902757619738752
|
|
28
|
+
IGHD2-21_star_01_22: 0.002902757619738752
|
|
29
|
+
IGHD2-21_star_01_23: 0.002902757619738752
|
|
30
|
+
IGHD2-21_star_01_24: 0.002902757619738752
|
|
31
|
+
IGHD2-21_star_01_25: 0.002902757619738752
|
|
32
|
+
IGHD2-21_star_01_26: 0.002902757619738752
|
|
33
|
+
IGHD2-21_star_01_27: 0.002902757619738752
|
|
34
|
+
IGHD2-21_star_01_3: 0.002902757619738752
|
|
35
|
+
IGHD2-21_star_01_4: 0.002902757619738752
|
|
36
|
+
IGHD2-21_star_01_5: 0.002177068214804064
|
|
37
|
+
IGHD2-21_star_01_6: 0.001451378809869376
|
|
38
|
+
IGHD2-21_star_01_7: 0.000725689404934688
|
|
39
|
+
IGHD2-21_star_01_8: 0.002902757619738752
|
|
40
|
+
IGHD2-21_star_01_9: 0.002902757619738752
|
|
41
|
+
insert_left_A: 0.1819202695115104
|
|
42
|
+
insert_left_C: 0.313307130825379
|
|
43
|
+
insert_left_G: 0.20213363279056712
|
|
44
|
+
insert_left_T: 0.22571588994946662
|
|
45
|
+
- !!python/object:python.hmmwriter.State
|
|
46
|
+
emissions:
|
|
47
|
+
probs:
|
|
48
|
+
A: 0.8883497389490509
|
|
49
|
+
C: 0.037216753683649705
|
|
50
|
+
G: 0.037216753683649705
|
|
51
|
+
T: 0.037216753683649705
|
|
52
|
+
track: nukes
|
|
53
|
+
extras:
|
|
54
|
+
ambiguous_char: N
|
|
55
|
+
ambiguous_emission_prob: 0.25
|
|
56
|
+
germline: A
|
|
57
|
+
name: insert_left_A
|
|
58
|
+
transitions:
|
|
59
|
+
IGHD2-21_star_01_0: 0.0030281854181225215
|
|
60
|
+
IGHD2-21_star_01_1: 0.0030281854181225215
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|
61
|
+
IGHD2-21_star_01_10: 0.0030281854181225215
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|
62
|
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IGHD2-21_star_01_11: 0.0030281854181225215
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|
63
|
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IGHD2-21_star_01_12: 0.0030281854181225215
|
|
64
|
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IGHD2-21_star_01_13: 0.0030281854181225215
|
|
65
|
+
IGHD2-21_star_01_14: 0.0030281854181225215
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|
66
|
+
IGHD2-21_star_01_15: 0.0030281854181225215
|
|
67
|
+
IGHD2-21_star_01_16: 0.0030281854181225215
|
|
68
|
+
IGHD2-21_star_01_17: 0.0030281854181225215
|
|
69
|
+
IGHD2-21_star_01_18: 0.0030281854181225215
|
|
70
|
+
IGHD2-21_star_01_19: 0.0030281854181225215
|
|
71
|
+
IGHD2-21_star_01_2: 0.0030281854181225215
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|
72
|
+
IGHD2-21_star_01_20: 0.0030281854181225215
|
|
73
|
+
IGHD2-21_star_01_21: 0.0030281854181225215
|
|
74
|
+
IGHD2-21_star_01_22: 0.0030281854181225215
|
|
75
|
+
IGHD2-21_star_01_23: 0.0030281854181225215
|
|
76
|
+
IGHD2-21_star_01_24: 0.0030281854181225215
|
|
77
|
+
IGHD2-21_star_01_25: 0.0030281854181225215
|
|
78
|
+
IGHD2-21_star_01_26: 0.0030281854181225215
|
|
79
|
+
IGHD2-21_star_01_27: 0.0030281854181225215
|
|
80
|
+
IGHD2-21_star_01_3: 0.0030281854181225215
|
|
81
|
+
IGHD2-21_star_01_4: 0.0030281854181225215
|
|
82
|
+
IGHD2-21_star_01_5: 0.0022711390635918914
|
|
83
|
+
IGHD2-21_star_01_6: 0.0015140927090612607
|
|
84
|
+
IGHD2-21_star_01_7: 0.0007570463545306304
|
|
85
|
+
IGHD2-21_star_01_8: 0.0030281854181225215
|
|
86
|
+
IGHD2-21_star_01_9: 0.0030281854181225215
|
|
87
|
+
insert_left_A: 0.1812652068126521
|
|
88
|
+
insert_left_C: 0.31217896728845634
|
|
89
|
+
insert_left_G: 0.2014057853473912
|
|
90
|
+
insert_left_T: 0.22490312697125353
|
|
91
|
+
- !!python/object:python.hmmwriter.State
|
|
92
|
+
emissions:
|
|
93
|
+
probs:
|
|
94
|
+
A: 0.037216753683649705
|
|
95
|
+
C: 0.8883497389490509
|
|
96
|
+
G: 0.037216753683649705
|
|
97
|
+
T: 0.037216753683649705
|
|
98
|
+
track: nukes
|
|
99
|
+
extras:
|
|
100
|
+
ambiguous_char: N
|
|
101
|
+
ambiguous_emission_prob: 0.25
|
|
102
|
+
germline: C
|
|
103
|
+
name: insert_left_C
|
|
104
|
+
transitions:
|
|
105
|
+
IGHD2-21_star_01_0: 0.0030281854181225215
|
|
106
|
+
IGHD2-21_star_01_1: 0.0030281854181225215
|
|
107
|
+
IGHD2-21_star_01_10: 0.0030281854181225215
|
|
108
|
+
IGHD2-21_star_01_11: 0.0030281854181225215
|
|
109
|
+
IGHD2-21_star_01_12: 0.0030281854181225215
|
|
110
|
+
IGHD2-21_star_01_13: 0.0030281854181225215
|
|
111
|
+
IGHD2-21_star_01_14: 0.0030281854181225215
|
|
112
|
+
IGHD2-21_star_01_15: 0.0030281854181225215
|
|
113
|
+
IGHD2-21_star_01_16: 0.0030281854181225215
|
|
114
|
+
IGHD2-21_star_01_17: 0.0030281854181225215
|
|
115
|
+
IGHD2-21_star_01_18: 0.0030281854181225215
|
|
116
|
+
IGHD2-21_star_01_19: 0.0030281854181225215
|
|
117
|
+
IGHD2-21_star_01_2: 0.0030281854181225215
|
|
118
|
+
IGHD2-21_star_01_20: 0.0030281854181225215
|
|
119
|
+
IGHD2-21_star_01_21: 0.0030281854181225215
|
|
120
|
+
IGHD2-21_star_01_22: 0.0030281854181225215
|
|
121
|
+
IGHD2-21_star_01_23: 0.0030281854181225215
|
|
122
|
+
IGHD2-21_star_01_24: 0.0030281854181225215
|
|
123
|
+
IGHD2-21_star_01_25: 0.0030281854181225215
|
|
124
|
+
IGHD2-21_star_01_26: 0.0030281854181225215
|
|
125
|
+
IGHD2-21_star_01_27: 0.0030281854181225215
|
|
126
|
+
IGHD2-21_star_01_3: 0.0030281854181225215
|
|
127
|
+
IGHD2-21_star_01_4: 0.0030281854181225215
|
|
128
|
+
IGHD2-21_star_01_5: 0.0022711390635918914
|
|
129
|
+
IGHD2-21_star_01_6: 0.0015140927090612607
|
|
130
|
+
IGHD2-21_star_01_7: 0.0007570463545306304
|
|
131
|
+
IGHD2-21_star_01_8: 0.0030281854181225215
|
|
132
|
+
IGHD2-21_star_01_9: 0.0030281854181225215
|
|
133
|
+
insert_left_A: 0.1812652068126521
|
|
134
|
+
insert_left_C: 0.31217896728845634
|
|
135
|
+
insert_left_G: 0.2014057853473912
|
|
136
|
+
insert_left_T: 0.22490312697125353
|
|
137
|
+
- !!python/object:python.hmmwriter.State
|
|
138
|
+
emissions:
|
|
139
|
+
probs:
|
|
140
|
+
A: 0.037216753683649705
|
|
141
|
+
C: 0.037216753683649705
|
|
142
|
+
G: 0.8883497389490509
|
|
143
|
+
T: 0.037216753683649705
|
|
144
|
+
track: nukes
|
|
145
|
+
extras:
|
|
146
|
+
ambiguous_char: N
|
|
147
|
+
ambiguous_emission_prob: 0.25
|
|
148
|
+
germline: G
|
|
149
|
+
name: insert_left_G
|
|
150
|
+
transitions:
|
|
151
|
+
IGHD2-21_star_01_0: 0.0030281854181225215
|
|
152
|
+
IGHD2-21_star_01_1: 0.0030281854181225215
|
|
153
|
+
IGHD2-21_star_01_10: 0.0030281854181225215
|
|
154
|
+
IGHD2-21_star_01_11: 0.0030281854181225215
|
|
155
|
+
IGHD2-21_star_01_12: 0.0030281854181225215
|
|
156
|
+
IGHD2-21_star_01_13: 0.0030281854181225215
|
|
157
|
+
IGHD2-21_star_01_14: 0.0030281854181225215
|
|
158
|
+
IGHD2-21_star_01_15: 0.0030281854181225215
|
|
159
|
+
IGHD2-21_star_01_16: 0.0030281854181225215
|
|
160
|
+
IGHD2-21_star_01_17: 0.0030281854181225215
|
|
161
|
+
IGHD2-21_star_01_18: 0.0030281854181225215
|
|
162
|
+
IGHD2-21_star_01_19: 0.0030281854181225215
|
|
163
|
+
IGHD2-21_star_01_2: 0.0030281854181225215
|
|
164
|
+
IGHD2-21_star_01_20: 0.0030281854181225215
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|
165
|
+
IGHD2-21_star_01_21: 0.0030281854181225215
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|
166
|
+
IGHD2-21_star_01_22: 0.0030281854181225215
|
|
167
|
+
IGHD2-21_star_01_23: 0.0030281854181225215
|
|
168
|
+
IGHD2-21_star_01_24: 0.0030281854181225215
|
|
169
|
+
IGHD2-21_star_01_25: 0.0030281854181225215
|
|
170
|
+
IGHD2-21_star_01_26: 0.0030281854181225215
|
|
171
|
+
IGHD2-21_star_01_27: 0.0030281854181225215
|
|
172
|
+
IGHD2-21_star_01_3: 0.0030281854181225215
|
|
173
|
+
IGHD2-21_star_01_4: 0.0030281854181225215
|
|
174
|
+
IGHD2-21_star_01_5: 0.0022711390635918914
|
|
175
|
+
IGHD2-21_star_01_6: 0.0015140927090612607
|
|
176
|
+
IGHD2-21_star_01_7: 0.0007570463545306304
|
|
177
|
+
IGHD2-21_star_01_8: 0.0030281854181225215
|
|
178
|
+
IGHD2-21_star_01_9: 0.0030281854181225215
|
|
179
|
+
insert_left_A: 0.1812652068126521
|
|
180
|
+
insert_left_C: 0.31217896728845634
|
|
181
|
+
insert_left_G: 0.2014057853473912
|
|
182
|
+
insert_left_T: 0.22490312697125353
|
|
183
|
+
- !!python/object:python.hmmwriter.State
|
|
184
|
+
emissions:
|
|
185
|
+
probs:
|
|
186
|
+
A: 0.037216753683649705
|
|
187
|
+
C: 0.037216753683649705
|
|
188
|
+
G: 0.037216753683649705
|
|
189
|
+
T: 0.8883497389490509
|
|
190
|
+
track: nukes
|
|
191
|
+
extras:
|
|
192
|
+
ambiguous_char: N
|
|
193
|
+
ambiguous_emission_prob: 0.25
|
|
194
|
+
germline: T
|
|
195
|
+
name: insert_left_T
|
|
196
|
+
transitions:
|
|
197
|
+
IGHD2-21_star_01_0: 0.0030281854181225215
|
|
198
|
+
IGHD2-21_star_01_1: 0.0030281854181225215
|
|
199
|
+
IGHD2-21_star_01_10: 0.0030281854181225215
|
|
200
|
+
IGHD2-21_star_01_11: 0.0030281854181225215
|
|
201
|
+
IGHD2-21_star_01_12: 0.0030281854181225215
|
|
202
|
+
IGHD2-21_star_01_13: 0.0030281854181225215
|
|
203
|
+
IGHD2-21_star_01_14: 0.0030281854181225215
|
|
204
|
+
IGHD2-21_star_01_15: 0.0030281854181225215
|
|
205
|
+
IGHD2-21_star_01_16: 0.0030281854181225215
|
|
206
|
+
IGHD2-21_star_01_17: 0.0030281854181225215
|
|
207
|
+
IGHD2-21_star_01_18: 0.0030281854181225215
|
|
208
|
+
IGHD2-21_star_01_19: 0.0030281854181225215
|
|
209
|
+
IGHD2-21_star_01_2: 0.0030281854181225215
|
|
210
|
+
IGHD2-21_star_01_20: 0.0030281854181225215
|
|
211
|
+
IGHD2-21_star_01_21: 0.0030281854181225215
|
|
212
|
+
IGHD2-21_star_01_22: 0.0030281854181225215
|
|
213
|
+
IGHD2-21_star_01_23: 0.0030281854181225215
|
|
214
|
+
IGHD2-21_star_01_24: 0.0030281854181225215
|
|
215
|
+
IGHD2-21_star_01_25: 0.0030281854181225215
|
|
216
|
+
IGHD2-21_star_01_26: 0.0030281854181225215
|
|
217
|
+
IGHD2-21_star_01_27: 0.0030281854181225215
|
|
218
|
+
IGHD2-21_star_01_3: 0.0030281854181225215
|
|
219
|
+
IGHD2-21_star_01_4: 0.0030281854181225215
|
|
220
|
+
IGHD2-21_star_01_5: 0.0022711390635918914
|
|
221
|
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IGHD2-21_star_01_6: 0.0015140927090612607
|
|
222
|
+
IGHD2-21_star_01_7: 0.0007570463545306304
|
|
223
|
+
IGHD2-21_star_01_8: 0.0030281854181225215
|
|
224
|
+
IGHD2-21_star_01_9: 0.0030281854181225215
|
|
225
|
+
insert_left_A: 0.1812652068126521
|
|
226
|
+
insert_left_C: 0.31217896728845634
|
|
227
|
+
insert_left_G: 0.2014057853473912
|
|
228
|
+
insert_left_T: 0.22490312697125353
|
|
229
|
+
- !!python/object:python.hmmwriter.State
|
|
230
|
+
emissions:
|
|
231
|
+
probs:
|
|
232
|
+
A: 0.8883497389490509
|
|
233
|
+
C: 0.0372167536836497
|
|
234
|
+
G: 0.0372167536836497
|
|
235
|
+
T: 0.0372167536836497
|
|
236
|
+
track: nukes
|
|
237
|
+
extras:
|
|
238
|
+
ambiguous_char: N
|
|
239
|
+
ambiguous_emission_prob: 0.25
|
|
240
|
+
germline: A
|
|
241
|
+
name: IGHD2-21_star_01_0
|
|
242
|
+
transitions:
|
|
243
|
+
IGHD2-21_star_01_1: 0.9565217391304348
|
|
244
|
+
end: 0.04347826086956522
|
|
245
|
+
- !!python/object:python.hmmwriter.State
|
|
246
|
+
emissions:
|
|
247
|
+
probs:
|
|
248
|
+
A: 0.03706732053242103
|
|
249
|
+
C: 0.03706732053242103
|
|
250
|
+
G: 0.8887980384027369
|
|
251
|
+
T: 0.03706732053242103
|
|
252
|
+
track: nukes
|
|
253
|
+
extras:
|
|
254
|
+
ambiguous_char: N
|
|
255
|
+
ambiguous_emission_prob: 0.25
|
|
256
|
+
germline: G
|
|
257
|
+
name: IGHD2-21_star_01_1
|
|
258
|
+
transitions:
|
|
259
|
+
IGHD2-21_star_01_2: 0.9565217391304348
|
|
260
|
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end: 0.04347826086956522
|
|
261
|
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- !!python/object:python.hmmwriter.State
|
|
262
|
+
emissions:
|
|
263
|
+
probs:
|
|
264
|
+
A: 0.03691788738119236
|
|
265
|
+
C: 0.8892463378564229
|
|
266
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592
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598
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|
607
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|
608
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germline: A
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|
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|
613
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|
614
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623
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624
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626
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629
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|
630
|
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|
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|
632
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|
640
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|
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645
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|
646
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654
|
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|
655
|
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|
656
|
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germline: C
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|
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|
658
|
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|
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|
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|
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|
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|
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|
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|
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ambiguous_emission_prob: 0.25
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|
672
|
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germline: C
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|
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nukes:
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|
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|
680
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- G
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