partis-bcr 1.0.11.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl → 1.0.12__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-1.0.12.data}/scripts/partis-test.py +6 -0
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/METADATA +1 -1
- {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/RECORD +647 -129
- 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
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