├── .cargo └── config ├── .git-credentials ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ ├── release.yaml │ ├── release_with_windows.yaml.save │ └── test.yaml ├── .gitignore ├── Cargo.lock ├── Cargo.toml ├── GUIDE ├── LICENSE.txt ├── README.md ├── cd_datasets ├── crates.dot ├── credits ├── Apache-2.0 ├── MPL-2.0-source_code_availabliity ├── MPL2.0 ├── acknowledgements ├── arrayref ├── chromium ├── cloudabi ├── fuchsia ├── instant ├── mach ├── num_enum ├── palaver ├── pasteboard ├── ring ├── tiny-skia └── webpki ├── datasets_medium_checksum ├── datasets_small_checksum ├── enclone_build ├── Cargo.toml ├── build.rs └── src │ ├── bin │ └── traceback1.rs │ └── lib.rs ├── enclone_denovo ├── Cargo.toml └── src │ ├── bin │ ├── 200mammals │ ├── abc_dump.rs.aside │ ├── abc_look.rs.aside │ ├── analyze_const.rs │ ├── denovo.rs │ ├── download_genbank_assembly.rs │ ├── download_isoseq.rs │ ├── download_mammals.rs │ ├── download_one_isoseq.rs │ ├── genomes_list │ ├── rare.rs.aside │ ├── score_ab.rs.aside │ ├── squeeze_novo.rs │ ├── sync_to_genome_list.rs │ ├── test_const_ighd.rs │ └── test_denovo.rs │ ├── const_ighd.rs │ ├── const_ighd_best_hits │ ├── const_ighd_initial_truth │ ├── const_motifs │ ├── genome_list │ ├── igha.data │ ├── ighd.data │ ├── ighe.data │ ├── ighg.data │ ├── ighm.data │ ├── igkc.data │ ├── iglc.data │ ├── isoseq_list │ ├── lib.rs │ ├── make_fwr3_freqs.rs │ ├── make_mammalian_fixed_len.rs │ ├── make_mammalian_pwms.rs │ ├── mammalian_fixed_len.rs │ ├── mammalian_fixed_len.table │ ├── mammalian_pwms.rs │ ├── mammalian_pwms.table │ ├── validation_data_notes │ └── vdj_features.rs ├── enclone_exec ├── Cargo.toml ├── LICENSE.txt ├── src │ └── bin │ │ └── enclone.rs ├── tests │ ├── enclone.testdata │ ├── enclone_test1.rs │ ├── enclone_test2.rs │ ├── enclone_test3.rs │ ├── enclone_test4.rs │ ├── test_comx.rs.aside │ ├── test_output │ ├── testdata.public.bcr.human │ ├── testdata.public.gex.human │ ├── testdata.public.tcr.human │ └── testdata.public.tcr.mouse └── testx │ ├── .gitignore │ └── inputs │ ├── 101287.binary.sha256 │ ├── 123077_cells.csv │ ├── 123077_cells.tsv │ ├── 123085.binary.sha256 │ ├── 123085_args │ ├── 123085_info.csv │ ├── 128024_cells.csv │ ├── bc_joint.csv │ ├── busted_regions.fa │ ├── flaky │ ├── README │ └── outs │ │ ├── all_contig_annotations.json │ │ └── genetic_demux_results │ │ ├── README │ │ └── clusters.tsv │ ├── flaky10 │ ├── README │ └── outs │ │ └── all_contig_annotations.json │ ├── flaky11 │ ├── README │ └── outs │ │ └── all_contig_annotations.json.lz4 │ ├── flaky12 │ ├── README │ └── outs │ │ └── all_contig_annotations.json.lz4 │ ├── flaky13 │ ├── README │ └── outs │ │ └── all_contig_annotations.json.lz4 │ ├── flaky2 │ ├── README │ └── outs │ │ └── all_contig_annotations.json │ ├── flaky3 │ ├── README │ └── outs │ │ └── all_contig_annotations.json │ ├── flaky4 │ ├── README │ └── outs │ │ └── all_contig_annotations.json │ ├── flaky5 │ ├── README │ └── outs │ │ └── all_contig_annotations.json │ ├── flaky6 │ ├── README │ └── outs │ │ └── all_contig_annotations.json.lz4 │ ├── flaky7 │ ├── README │ └── outs │ │ └── all_contig_annotations.json.lz4 │ ├── flaky8a │ ├── README │ └── outs │ │ └── all_contig_annotations.json │ ├── flaky8b │ ├── README │ └── outs │ │ └── all_contig_annotations.json │ ├── flaky9 │ ├── README │ └── outs │ │ └── all_contig_annotations.json.lz4 │ ├── gamma_delta1 │ └── outs │ │ └── all_contig_annotations.json │ ├── meta1.csv │ ├── meta2.csv │ ├── outputs │ ├── enclone_annotated_example_test1_output │ ├── enclone_dtest10_output │ ├── enclone_dtest11_output │ ├── enclone_dtest12_output │ ├── enclone_dtest13_output │ ├── enclone_dtest14_output │ ├── enclone_dtest15_output │ ├── enclone_dtest1_output │ ├── enclone_dtest2_output │ ├── enclone_dtest4_output │ ├── enclone_dtest5_output │ ├── enclone_dtest6_output │ ├── enclone_dtest7_output │ ├── enclone_dtest8_output │ ├── enclone_dtest9_output │ ├── enclone_ext_test10_output │ ├── enclone_ext_test11_output │ ├── enclone_ext_test12_output │ ├── enclone_ext_test13_output │ ├── enclone_ext_test14_output │ ├── enclone_ext_test16_output │ ├── enclone_ext_test17_output │ ├── enclone_ext_test18_output │ ├── enclone_ext_test1_output │ ├── enclone_ext_test20_output │ ├── enclone_ext_test21_output │ ├── enclone_ext_test22_output │ ├── enclone_ext_test24_output │ ├── enclone_ext_test25_output │ ├── enclone_ext_test27_output │ ├── enclone_ext_test28_output │ ├── enclone_ext_test29_output │ ├── enclone_ext_test2_output │ ├── enclone_ext_test31_output │ ├── enclone_ext_test32_output │ ├── enclone_ext_test33_output │ ├── enclone_ext_test34_output │ ├── enclone_ext_test35_output │ ├── enclone_ext_test36_output │ ├── enclone_ext_test3_output │ ├── enclone_ext_test4_output │ ├── enclone_ext_test5_output │ ├── enclone_ext_test6_output │ ├── enclone_ext_test7_output │ ├── enclone_ext_test8_output │ ├── enclone_ext_test9_output │ ├── enclone_gtest10_output │ ├── enclone_gtest11_output │ ├── enclone_gtest12_output │ ├── enclone_gtest13_output │ ├── enclone_gtest14_output │ ├── enclone_gtest15_output │ ├── enclone_gtest16_output │ ├── enclone_gtest17_output │ ├── enclone_gtest18_output │ ├── enclone_gtest19_output │ ├── enclone_gtest1_output │ ├── enclone_gtest20_output │ ├── enclone_gtest2_output │ ├── enclone_gtest3_output │ ├── enclone_gtest4_output │ ├── enclone_gtest5_output │ ├── enclone_gtest6_output │ ├── enclone_gtest7_output │ ├── enclone_gtest8_output │ ├── enclone_gtest9_output │ ├── enclone_internal_test1_output │ ├── enclone_internal_test2_output │ ├── enclone_internal_test3_output │ ├── enclone_test100_output │ ├── enclone_test101_output │ ├── enclone_test103_output │ ├── enclone_test104_output │ ├── enclone_test105_output │ ├── enclone_test106_output │ ├── enclone_test107_output │ ├── enclone_test108_output │ ├── enclone_test109_output │ ├── enclone_test10_output │ ├── enclone_test110_output │ ├── enclone_test112_output │ ├── enclone_test113_output │ ├── enclone_test114_output │ ├── enclone_test115_output │ ├── enclone_test116_output │ ├── enclone_test117_output │ ├── enclone_test118_output │ ├── enclone_test119_output │ ├── enclone_test11_output │ ├── enclone_test120_output │ ├── enclone_test121_output │ ├── enclone_test122_output │ ├── enclone_test123_output │ ├── enclone_test124_output │ ├── enclone_test125_output │ ├── enclone_test126_output │ ├── enclone_test127_output │ ├── enclone_test128_output │ ├── enclone_test129_output │ ├── enclone_test12_output │ ├── enclone_test130_output │ ├── enclone_test131_output │ ├── enclone_test132_output │ ├── enclone_test133_output │ ├── enclone_test134_output │ ├── enclone_test135_output │ ├── enclone_test136_output │ ├── enclone_test137_output │ ├── enclone_test138_output │ ├── enclone_test139_output │ ├── enclone_test13_output │ ├── enclone_test140_output │ ├── enclone_test141_output │ ├── enclone_test142_output │ ├── enclone_test143_output │ ├── enclone_test144_output │ ├── enclone_test145_output │ ├── enclone_test146_output │ ├── enclone_test147_output │ ├── enclone_test149_output │ ├── enclone_test14_output │ ├── enclone_test150_output │ ├── enclone_test151_output │ ├── enclone_test152_output │ ├── enclone_test153_output │ ├── enclone_test154_output │ ├── enclone_test155_output │ ├── enclone_test156_output │ ├── enclone_test157_output │ ├── enclone_test158_output │ ├── enclone_test159_output │ ├── enclone_test15_output │ ├── enclone_test160_output │ ├── enclone_test161_output │ ├── enclone_test162_output │ ├── enclone_test163_output │ ├── enclone_test164_output │ ├── enclone_test165_output │ ├── enclone_test166_output │ ├── enclone_test168_output │ ├── enclone_test169_output │ ├── enclone_test16_output │ ├── enclone_test170_output │ ├── enclone_test171_output │ ├── enclone_test173_output │ ├── enclone_test174_output │ ├── enclone_test175_output │ ├── enclone_test176_output │ ├── enclone_test177_output │ ├── enclone_test178_output │ ├── enclone_test179_output │ ├── enclone_test17_output │ ├── enclone_test180_output │ ├── enclone_test181_output │ ├── enclone_test182_output │ ├── enclone_test183_output │ ├── enclone_test184_output │ ├── enclone_test185_output │ ├── enclone_test186_output │ ├── enclone_test187_output │ ├── enclone_test188_output │ ├── enclone_test189_output │ ├── enclone_test18_output │ ├── enclone_test190_output │ ├── enclone_test191_output │ ├── enclone_test192_output │ ├── enclone_test196_output │ ├── enclone_test198_output │ ├── enclone_test199_output │ ├── enclone_test19_output │ ├── enclone_test1_output │ ├── enclone_test200_output │ ├── enclone_test201_output │ ├── enclone_test203_output │ ├── enclone_test204_output │ ├── enclone_test205_output │ ├── enclone_test206_output │ ├── enclone_test207_output │ ├── enclone_test208_output │ ├── enclone_test209_output │ ├── enclone_test20_output │ ├── enclone_test210_output │ ├── enclone_test211_output │ ├── enclone_test212_output │ ├── enclone_test213_output │ ├── enclone_test214_output │ ├── enclone_test215_output │ ├── enclone_test216_output │ ├── enclone_test217_output │ ├── enclone_test218_output │ ├── enclone_test219_output │ ├── enclone_test21_output │ ├── enclone_test220_output │ ├── enclone_test221_output │ ├── enclone_test223_output │ ├── enclone_test224_output │ ├── enclone_test225_output │ ├── enclone_test226_output │ ├── enclone_test227_output │ ├── enclone_test228_output │ ├── enclone_test229_output │ ├── enclone_test22_output │ ├── enclone_test230_output │ ├── enclone_test231_output │ ├── enclone_test233_output │ ├── enclone_test234_output │ ├── enclone_test235_output │ ├── enclone_test236_output │ ├── enclone_test238_output │ ├── enclone_test239_output │ ├── enclone_test23_output │ ├── enclone_test240_output │ ├── enclone_test241_output │ ├── enclone_test242_output │ ├── enclone_test244_output │ ├── enclone_test245_output │ ├── enclone_test246_output │ ├── enclone_test247_output │ ├── enclone_test248_output │ ├── enclone_test249_output │ ├── enclone_test24_output │ ├── enclone_test250_output │ ├── enclone_test251_output │ ├── enclone_test252_output │ ├── enclone_test254_output │ ├── enclone_test255_output │ ├── enclone_test256_output │ ├── enclone_test257_output │ ├── enclone_test25_output │ ├── enclone_test260_output │ ├── enclone_test261_output │ ├── enclone_test262_output │ ├── enclone_test263_output │ ├── enclone_test264_output │ ├── enclone_test265_output │ ├── enclone_test266_output │ ├── enclone_test267_output │ ├── enclone_test268_output │ ├── enclone_test269_output │ ├── enclone_test26_output │ ├── enclone_test270_output │ ├── enclone_test272_output │ ├── enclone_test273_output │ ├── enclone_test274_output │ ├── enclone_test275_output │ ├── enclone_test277_output │ ├── enclone_test278_output │ ├── enclone_test279_output │ ├── enclone_test27_output │ ├── enclone_test281_output │ ├── enclone_test282_output │ ├── enclone_test283_output │ ├── enclone_test284_output │ ├── enclone_test285_output │ ├── enclone_test287_output │ ├── enclone_test288_output │ ├── enclone_test289_output │ ├── enclone_test28_output │ ├── enclone_test290_output │ ├── enclone_test291_output │ ├── enclone_test293_output │ ├── enclone_test295_output │ ├── enclone_test296_output │ ├── enclone_test297_output │ ├── enclone_test298_output │ ├── enclone_test299_output │ ├── enclone_test29_output │ ├── enclone_test2_output │ ├── enclone_test300_output │ ├── enclone_test301_output │ ├── enclone_test302_output │ ├── enclone_test303_output │ ├── enclone_test304_output │ ├── enclone_test30_output │ ├── enclone_test31_output │ ├── enclone_test32_output │ ├── enclone_test33_output │ ├── enclone_test34_output │ ├── enclone_test35_output │ ├── enclone_test36_output │ ├── enclone_test37_output │ ├── enclone_test38_output │ ├── enclone_test39_output │ ├── enclone_test3_output │ ├── enclone_test40_output │ ├── enclone_test41_output │ ├── enclone_test44_output │ ├── enclone_test45_output │ ├── enclone_test46_output │ ├── enclone_test48_output │ ├── enclone_test49_output │ ├── enclone_test4_output │ ├── enclone_test52_output │ ├── enclone_test53_output │ ├── enclone_test55_output │ ├── enclone_test56_output │ ├── enclone_test57_output │ ├── enclone_test58_output │ ├── enclone_test59_output │ ├── enclone_test5_output │ ├── enclone_test60_output │ ├── enclone_test61_output │ ├── enclone_test62_output │ ├── enclone_test63_output │ ├── enclone_test64_output │ ├── enclone_test65_output │ ├── enclone_test66_output │ ├── enclone_test67_output │ ├── enclone_test68_output │ ├── enclone_test69_output │ ├── enclone_test6_output │ ├── enclone_test71_output │ ├── enclone_test72_output │ ├── enclone_test73_output │ ├── enclone_test74_output │ ├── enclone_test75_output │ ├── enclone_test76_output │ ├── enclone_test77_output │ ├── enclone_test7_output │ ├── enclone_test81_output │ ├── enclone_test82_output │ ├── enclone_test83_output │ ├── enclone_test84_output │ ├── enclone_test85_output │ ├── enclone_test86_output │ ├── enclone_test87_output │ ├── enclone_test88_output │ ├── enclone_test89_output │ ├── enclone_test8_output │ ├── enclone_test90_output │ ├── enclone_test91_output │ ├── enclone_test92_output │ ├── enclone_test93_output │ ├── enclone_test94_output │ ├── enclone_test95_output │ ├── enclone_test96_output │ ├── enclone_test97_output │ ├── enclone_test98_output │ ├── enclone_test99_output │ ├── enclone_test9_output │ └── test_honey.svg │ ├── test11_meta │ ├── test35_bc │ └── test35_meta ├── enclone_help ├── Cargo.toml ├── LICENSE.txt └── src │ ├── enclone_css_v2.css │ ├── example1 │ ├── example2 │ ├── help1.rs │ ├── help2.rs │ ├── help3.rs │ ├── help4.rs │ ├── help5.rs │ ├── help_utils.rs │ └── lib.rs ├── enclone_main ├── Cargo.toml ├── LICENSE.txt └── src │ ├── determine_ref.rs │ ├── enclone.test │ ├── lib.rs │ ├── main_enclone.rs │ ├── opt_d_val.rs │ ├── sec_mem.rs │ ├── setup.rs │ ├── stop.rs │ └── subset.rs ├── enclone_paper ├── Cargo.toml ├── data │ ├── CoV-AbDab_040322.csv.gz │ ├── README │ ├── curves_1.csv │ ├── curves_2.csv │ ├── curves_3.csv │ ├── curves_4.csv │ ├── light_chain_coherence.log │ ├── mat.575142 │ ├── olga.yml │ ├── seqlogofig.csv │ └── test_data.csv ├── error_rate ├── make_release ├── src │ ├── README │ ├── bin │ │ ├── assess_clonotyping.rs │ │ ├── build_clonotyping_inputs.rs │ │ ├── covid.rs │ │ ├── dataset_table.rs │ │ ├── hl_similarity.rs │ │ ├── insertion_analysis.rs │ │ ├── light_chain_coherence.rs │ │ ├── olga.seqs │ │ ├── olga_splice.rs │ │ ├── pgen_analysis.rs │ │ ├── pgen_compute.rs │ │ ├── plot_error_rate.rs │ │ ├── private_light_chain_analysis.rs │ │ ├── public_light_chain_analysis.rs │ │ ├── sim_dup.rs │ │ └── weighted_light_chain_analysis.rs │ ├── enclone.testdata.bcr.gex │ ├── lib.rs │ ├── partis │ │ └── README │ ├── scoper │ │ ├── README │ │ ├── autopilot.R │ │ └── autopilot_master.sh │ └── vis │ │ └── curves.R ├── test_data.csv └── which_code_does_what ├── enclone_tail ├── Cargo.toml ├── LICENSE.txt └── src │ ├── align_n.rs │ ├── alluvial_fb.rs │ ├── assign_cell_color.rs │ ├── cat_var.rs │ ├── circles_to_svg.rs │ ├── clustal.rs │ ├── colors.rs │ ├── convert_svg_to_png.rs │ ├── display_tree.rs │ ├── fasta.rs │ ├── fate.rs │ ├── group.rs │ ├── group_colors.rs │ ├── grouper.rs │ ├── hex.rs │ ├── keeper_group.rs │ ├── legend.rs │ ├── lib.rs │ ├── mammalian_fixed_len.rs │ ├── mammalian_fixed_len.table │ ├── neighbor.rs │ ├── newick.rs │ ├── pack_circles.rs │ ├── parseable.rs │ ├── phylip.rs │ ├── plot.rs │ ├── plot_points.rs │ ├── plot_utils.rs │ ├── polygon.rs │ ├── print_clonotypes │ ├── build_table_stuff.rs │ ├── finish_table.rs │ ├── gene_scan.rs │ ├── mod.rs │ ├── print_utils1.rs │ ├── print_utils2.rs │ ├── print_utils3.rs │ ├── print_utils4.rs │ ├── print_utils5.rs │ ├── proc_cvar_auto.rs │ ├── proc_lvar2.rs │ └── proc_lvar_auto.rs │ ├── print_dataset_vars.rs │ ├── print_stats.rs │ ├── requirements.rs │ ├── sens_spec.rs │ ├── set_speakers.rs │ ├── sim_mat_plot.rs │ ├── string_width.rs │ ├── tail.rs │ ├── ticks.rs │ └── tree.rs ├── enclone_testlist ├── Cargo.toml └── src │ ├── enclone.test │ ├── enclone.test.tcr │ ├── enclone.test2 │ ├── enclone.test_details │ ├── enclone.testdata │ ├── enclone.testdata.bcr.gex │ ├── enclone.testdata.mouse │ ├── enclone.testdata.targeted.bcr │ ├── enclone.testdata.tcr │ ├── enclone.testdata3 │ ├── enclone.testlist.all │ ├── lib.rs │ ├── main_testlist.rs │ ├── testdata.public.bcr.human │ ├── testdata.public.gex.human │ ├── testdata.public.tcr.human │ └── testdata.public.tcr.mouse ├── enclone_tools ├── Cargo.toml ├── LICENSE.txt └── src │ ├── bin │ ├── README │ ├── annotate_seq.rs │ ├── annotate_seqs.rs │ ├── antibody_antigen_structures │ ├── build_help_pages.rs │ ├── cdr_truth_data.fasta │ ├── cdr_truth_data.rs │ ├── check_versions.rs │ ├── convert_fasta.rs │ ├── diff_enclone.rs │ ├── diff_enclone_ann.rs │ ├── display_csv.rs │ ├── download_pdbs.rs │ ├── download_pdbs2.rs │ ├── dup_crates.rs │ ├── expand_ranges.rs │ ├── fetch_barcode_reads.rs │ ├── filtered_from_json.rs │ ├── json_from_filtered.rs │ ├── json_from_ireceptor.rs │ ├── melt.rs │ ├── merge_html.rs │ ├── mine_abybank.rs │ ├── minimal_fail.rs │ ├── pdb2.rs │ ├── pdb_print.rs │ ├── pdb_test.rs │ ├── print_mammalian_fixed_len.rs │ ├── print_mammalian_pwms.rs │ ├── release_nanny.rs │ ├── shrink_fasta.rs │ ├── shrink_json.rs │ ├── start_release.rs │ ├── test_beta_cdf.rs │ └── test_expr.rs │ ├── html.rs │ ├── lib.rs │ ├── pdb.rs │ └── run_test.rs ├── enclone_version ├── Cargo.toml ├── LICENSE.txt └── src │ └── lib.rs ├── fonts ├── DejaVuLGCSansMono-Bold.ttf ├── DejaVuLGCSansMono.ttf ├── LiberationSans-Regular.ttf ├── README ├── SIL_Open_Font_License.txt └── google_font_test.html ├── img ├── by_dataset.svg ├── cat_var.svg ├── cell_bits.svg ├── clono.svg ├── cred_gex_dist.png ├── enclone_annotated_example.svg ├── enclone_banner.png ├── iso.svg ├── quad_hive.svg ├── samples.svg ├── sim_mat_plot.svg ├── twin_plot.svg ├── two_genes.svg ├── var.png ├── visual1.png ├── visual2.png ├── visual_archive1.png └── what_is_a_clonotype.svg ├── index.html ├── install.sh ├── install_debug.sh ├── internal_docs ├── PREHISTORY ├── data_transfer ├── gex_files └── release_instructions ├── local_view ├── pages ├── README ├── analysis.html.src.aside ├── auto │ ├── DO_NOT_MANUALLY_EDIT_THESE_FILES │ ├── align_example.html │ ├── cellranger.html │ ├── clonotype_with_gex.html │ ├── d_gene_example1.html │ ├── d_gene_example1b.html │ ├── d_gene_example2.html │ ├── d_genes.html │ ├── default_filters.html │ ├── dev.html │ ├── expanded.html │ ├── features.html │ ├── foursie1.html │ ├── foursie2.html │ ├── help.all.html │ ├── help.amino.html │ ├── help.color.html │ ├── help.command.html │ ├── help.cvars.html │ ├── help.display.html │ ├── help.example1.html │ ├── help.example2.html │ ├── help.faq.html │ ├── help.filter.html │ ├── help.glossary.html │ ├── help.how.html │ ├── help.indels.html │ ├── help.input.html │ ├── help.input_tech.html │ ├── help.lvars.html │ ├── help.main.html │ ├── help.parseable.html │ ├── help.quick.html │ ├── help.setup.html │ ├── help.special.html │ ├── heuristics.html │ ├── history.html │ ├── illusory1.html │ ├── illusory2.html │ ├── illusory3.html │ ├── illusory4.html │ ├── illusory5.html │ ├── innate.html │ ├── install_issues.html │ ├── installation_details.html │ ├── jun_align_example.html │ ├── mait_example.html │ ├── plot.html │ ├── tree.html │ ├── tree_example.html │ ├── var_def.html │ ├── variable_demo.html │ ├── variable_demo2.html │ ├── variables.html │ ├── vddj.html │ ├── visual.html │ └── windows.html ├── cellranger.html.src ├── d_genes.html.src ├── default_filters.html.src ├── dev.html.src ├── enclone.css ├── enclone_css_v2.css ├── expanded.html.src ├── features.html.src ├── fetching_test_datasets.html.keeping_but_not_using_now ├── heuristics.html.src ├── history.html.src ├── innate.html.src ├── 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