├── .dockerignore ├── .flake8 ├── .github └── workflows │ ├── ci.yaml │ └── release.yaml ├── .gitignore ├── CHANGELOG.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── README.md ├── justfile ├── make_prg ├── __init__.py ├── __main__.py ├── from_msa │ ├── __init__.py │ ├── cluster_sequences.py │ └── interval_partition.py ├── prg_builder.py ├── recursion_tree.py ├── subcommands │ ├── __init__.py │ ├── from_msa.py │ ├── output_type.py │ └── update.py ├── update │ ├── MLPath.py │ ├── __init__.py │ ├── denovo_variants.py │ └── update_shared_data.py └── utils │ ├── __init__.py │ ├── gfa.py │ ├── input_output_files.py │ ├── io_utils.py │ ├── mafft-linux64 │ ├── mafft.bat │ └── mafftdir │ │ ├── bin │ │ └── mafft │ │ └── libexec │ │ ├── addsingle │ │ ├── contrafoldwrap │ │ ├── countlen │ │ ├── dash_alignments │ │ ├── dash_client │ │ ├── dash_sequences.fa │ │ ├── disttbfast │ │ ├── dndblast │ │ ├── dndfast7 │ │ ├── dndpre │ │ ├── dvtditr │ │ ├── f2cl │ │ ├── filter │ │ ├── getlag │ │ ├── hat3 │ │ ├── hex2maffttext │ │ ├── mafft-distance │ │ ├── mafft-homologs.1 │ │ ├── mafft-profile │ │ ├── mafft.1 │ │ ├── mafftash_premafft.pl │ │ ├── maffttext2hex │ │ ├── makedirectionlist │ │ ├── mccaskillwrap │ │ ├── multi2hat3s │ │ ├── nodepair │ │ ├── pairash │ │ ├── pairlocalalign │ │ ├── regtable2seq │ │ ├── replaceu │ │ ├── restoreu │ │ ├── score │ │ ├── seekquencer_premafft.pl │ │ ├── seq2regtable │ │ ├── setcore │ │ ├── setdirection │ │ ├── sextet5 │ │ ├── splittbfast │ │ ├── tbfast │ │ └── version │ ├── misc.py │ ├── msa_aligner.py │ ├── prg_encoder.py │ ├── recursive_tree_drawer.py │ └── seq_utils.py ├── poetry.lock ├── pyproject.toml ├── sample_example ├── README.md ├── denovo_paths │ └── denovo_paths.txt ├── msas │ ├── GC00006032.fa │ └── GC00010897.fa └── run_make_prg_on_sample_example.sh ├── scripts └── build_precompiled_binary │ ├── README.md │ └── build_precompiled_binary.sh └── tests ├── data ├── make_prg_from_msa │ ├── nested_snps_deletion.fa │ └── nested_snps_seq_backgrounds.fa ├── prg_builder │ └── write_prg │ │ ├── sample.truth.bin │ │ └── sample.truth.prg.fa ├── update │ ├── denovo_paths.txt │ └── empty_denovo_paths.txt └── utils │ ├── create_new_sequences_file │ └── new_sequences.truth.fa │ ├── gfa │ └── big_bang.truth.gfa │ ├── input_output_files │ └── concatenate_text_files │ │ ├── concatenated.truth.txt │ │ ├── file1.txt │ │ ├── file2.txt │ │ └── file3.txt │ └── io_utils │ ├── load_alignment_file │ ├── sample_msa.fa │ └── sample_msa.fa.gz │ └── zip_set_of_files │ └── files.truth.zip ├── from_msa ├── test_cluster_sequences.py └── test_interval_partition.py ├── integration_tests ├── data │ ├── a_column_full_of_Ns.fa │ ├── amira_MSAs │ │ ├── alsB.fasta │ │ ├── glpG.fasta │ │ └── group_18516.fasta │ ├── contains_RYKMSW.fa │ ├── contains_n.fa │ ├── contains_n_and_RYKMSW.fa │ ├── contains_n_no_variants.fa │ ├── fails_2.fa │ ├── match.fa │ ├── match.fa.gz │ ├── match.nonmatch.fa │ ├── match.nonmatch.match.fa │ ├── match.nonmatch.match_update │ │ └── denovo_paths.txt │ ├── match.nonmatch.shortmatch.fa │ ├── match.staggereddash.fa │ ├── match_bin_only.fa │ ├── match_gfa_only.fa │ ├── match_prg_only.fa │ ├── match_update_complex │ │ └── denovo_paths.txt │ ├── match_update_simple │ │ └── denovo_paths.txt │ ├── match_update_simple_bin_only │ │ └── denovo_paths.txt │ ├── match_update_simple_gfa_only │ │ └── denovo_paths.txt │ ├── match_update_simple_prg_only │ │ └── denovo_paths.txt │ ├── match_update_simple_with_long_deletion │ │ └── denovo_paths.txt │ ├── nested_snps_deletion.fa │ ├── nested_snps_seq_backgrounds.fa │ ├── nested_snps_seq_backgrounds_more_seqs.fa │ ├── nested_snps_seq_backgrounds_update │ │ └── denovo_paths.txt │ ├── nonmatch.fa │ ├── nonmatch.match.fa │ ├── nonmatch.shortmatch.fa │ ├── sample_example │ │ ├── GC00006032.fa │ │ └── GC00010897.fa │ ├── sample_example_update │ │ └── denovo_paths.txt │ ├── several │ │ ├── match.fa │ │ ├── match.nonmatch.fa │ │ ├── match.nonmatch.match.fa │ │ └── match.nonmatch.shortmatch.fa │ ├── several_compressed │ │ ├── match.fa.gz │ │ ├── match.nonmatch.fa.gz │ │ ├── match.nonmatch.match.fa.gz │ │ └── match.nonmatch.shortmatch.fa │ ├── several_empty │ │ ├── empty.fa │ │ ├── match.fa │ │ ├── match.nonmatch.fa │ │ └── match.nonmatch.match.fa │ ├── shortmatch.nonmatch.fa │ ├── shortmatch.nonmatch.match.fa │ ├── strict_insertions_and_deletions_update │ │ └── denovo_paths.txt │ ├── truth_output │ │ ├── a_column_full_of_Ns │ │ │ ├── a_column_full_of_Ns.prg.bin │ │ │ ├── a_column_full_of_Ns.prg.fa │ │ │ ├── a_column_full_of_Ns.prg.gfa │ │ │ └── a_column_full_of_Ns.update_DS.zip │ │ ├── amira_MSAs │ │ │ ├── amira_MSAs.prg.bin.zip │ │ │ ├── amira_MSAs.prg.fa │ │ │ ├── amira_MSAs.prg.gfa.zip │ │ │ └── amira_MSAs.update_DS.zip │ │ ├── contains_RYKMSW │ │ │ ├── contains_RYKMSW.prg.bin │ │ │ ├── contains_RYKMSW.prg.fa │ │ │ ├── contains_RYKMSW.prg.gfa │ │ │ └── contains_RYKMSW.update_DS.zip │ │ ├── contains_n │ │ │ ├── contains_n.prg.bin │ │ │ ├── contains_n.prg.fa │ │ │ ├── contains_n.prg.gfa │ │ │ └── contains_n.update_DS.zip │ │ ├── contains_n_and_RYKMSW │ │ │ ├── contains_n_and_RYKMSW.prg.bin │ │ │ ├── contains_n_and_RYKMSW.prg.fa │ │ │ ├── contains_n_and_RYKMSW.prg.gfa │ │ │ └── contains_n_and_RYKMSW.update_DS.zip │ │ ├── contains_n_no_variants │ │ │ ├── contains_n_no_variants.prg.bin │ │ │ ├── contains_n_no_variants.prg.fa │ │ │ ├── contains_n_no_variants.prg.gfa │ │ │ └── contains_n_no_variants.update_DS.zip │ │ ├── match.nonmatch.match │ │ │ ├── match.nonmatch.match.prg.bin │ │ │ ├── match.nonmatch.match.prg.fa │ │ │ ├── match.nonmatch.match.prg.gfa │ │ │ └── match.nonmatch.match.update_DS.zip │ │ ├── match.nonmatch.shortmatch │ │ │ ├── match.nonmatch.shortmatch.prg.bin │ │ │ ├── match.nonmatch.shortmatch.prg.fa │ │ │ ├── match.nonmatch.shortmatch.prg.gfa │ │ │ └── match.nonmatch.shortmatch.update_DS.zip │ │ ├── match.nonmatch │ │ │ ├── match.nonmatch.prg.bin │ │ │ ├── match.nonmatch.prg.fa │ │ │ ├── match.nonmatch.prg.gfa │ │ │ └── match.nonmatch.update_DS.zip │ │ ├── match.staggereddash │ │ │ ├── match.staggereddash.prg.bin │ │ │ ├── match.staggereddash.prg.fa │ │ │ ├── match.staggereddash.prg.gfa │ │ │ └── match.staggereddash.update_DS.zip │ │ ├── match │ │ │ ├── match.prg.bin │ │ │ ├── match.prg.fa │ │ │ ├── match.prg.gfa │ │ │ └── match.update_DS.zip │ │ ├── match_bin_only │ │ │ └── match_bin_only.prg.bin │ │ ├── match_compressed │ │ │ ├── match_compressed.prg.bin │ │ │ ├── match_compressed.prg.fa │ │ │ ├── match_compressed.prg.gfa │ │ │ └── match_compressed.update_DS.zip │ │ ├── match_gfa_only │ │ │ └── match_gfa_only.prg.gfa │ │ ├── match_overwrite │ │ │ ├── match.prg.bin │ │ │ ├── match.prg.fa │ │ │ ├── match.prg.gfa │ │ │ └── match.update_DS.zip │ │ ├── match_prg_only │ │ │ ├── match_prg_only.prg.fa │ │ │ └── match_prg_only.update_DS.zip │ │ ├── nested_snps_deletion │ │ │ ├── nested_snps_deletion.prg.bin │ │ │ ├── nested_snps_deletion.prg.fa │ │ │ ├── nested_snps_deletion.prg.gfa │ │ │ └── nested_snps_deletion.update_DS.zip │ │ ├── nested_snps_seq_backgrounds │ │ │ ├── nested_snps_seq_backgrounds.prg.bin │ │ │ ├── nested_snps_seq_backgrounds.prg.fa │ │ │ ├── nested_snps_seq_backgrounds.prg.gfa │ │ │ └── nested_snps_seq_backgrounds.update_DS.zip │ │ ├── nested_snps_seq_backgrounds_more_seqs │ │ │ ├── nested_snps_seq_backgrounds_more_seqs.prg.bin │ │ │ ├── nested_snps_seq_backgrounds_more_seqs.prg.fa │ │ │ ├── nested_snps_seq_backgrounds_more_seqs.prg.gfa │ │ │ └── nested_snps_seq_backgrounds_more_seqs.update_DS.zip │ │ ├── nonmatch.match │ │ │ ├── nonmatch.match.prg.bin │ │ │ ├── nonmatch.match.prg.fa │ │ │ ├── nonmatch.match.prg.gfa │ │ │ └── nonmatch.match.update_DS.zip │ │ ├── nonmatch.shortmatch │ │ │ ├── nonmatch.shortmatch.prg.bin │ │ │ ├── nonmatch.shortmatch.prg.fa │ │ │ ├── nonmatch.shortmatch.prg.gfa │ │ │ └── nonmatch.shortmatch.update_DS.zip │ │ ├── nonmatch │ │ │ ├── nonmatch.prg.bin │ │ │ ├── nonmatch.prg.fa │ │ │ ├── nonmatch.prg.gfa │ │ │ └── nonmatch.update_DS.zip │ │ ├── sample_example │ │ │ ├── sample_example.prg.bin.zip │ │ │ ├── sample_example.prg.fa │ │ │ ├── sample_example.prg.gfa.zip │ │ │ └── sample_example.update_DS.zip │ │ ├── several │ │ │ ├── several.prg.bin.zip │ │ │ ├── several.prg.fa │ │ │ ├── several.prg.gfa.zip │ │ │ └── several.update_DS.zip │ │ ├── several_compressed │ │ │ ├── several_compressed.prg.bin.zip │ │ │ ├── several_compressed.prg.fa │ │ │ ├── several_compressed.prg.gfa.zip │ │ │ └── several_compressed.update_DS.zip │ │ ├── shortmatch.nonmatch.match │ │ │ ├── shortmatch.nonmatch.match.prg.bin │ │ │ ├── shortmatch.nonmatch.match.prg.fa │ │ │ ├── shortmatch.nonmatch.match.prg.gfa │ │ │ └── shortmatch.nonmatch.match.update_DS.zip │ │ └── shortmatch.nonmatch │ │ │ ├── shortmatch.nonmatch.prg.bin │ │ │ ├── shortmatch.nonmatch.prg.fa │ │ │ ├── shortmatch.nonmatch.prg.gfa │ │ │ └── shortmatch.nonmatch.update_DS.zip │ └── truth_output_update │ │ ├── match.nonmatch.match_update │ │ ├── match.nonmatch.match_update.prg.bin │ │ ├── match.nonmatch.match_update.prg.fa │ │ ├── match.nonmatch.match_update.prg.gfa │ │ └── match.nonmatch.match_update.update_DS.zip │ │ ├── match_update_complex │ │ ├── match_update_complex.prg.bin │ │ ├── match_update_complex.prg.fa │ │ ├── match_update_complex.prg.gfa │ │ └── match_update_complex.update_DS.zip │ │ ├── match_update_simple │ │ ├── match_update_simple.prg.bin │ │ ├── match_update_simple.prg.fa │ │ ├── match_update_simple.prg.gfa │ │ └── match_update_simple.update_DS.zip │ │ ├── match_update_simple_bin_only │ │ └── match_update_simple_bin_only.prg.bin │ │ ├── match_update_simple_gfa_only │ │ └── match_update_simple_gfa_only.prg.gfa │ │ ├── match_update_simple_prg_only │ │ ├── match_update_simple_prg_only.prg.fa │ │ └── match_update_simple_prg_only.update_DS.zip │ │ ├── match_update_simple_with_long_deletion │ │ ├── match_update_simple_with_long_deletion.prg.bin │ │ ├── match_update_simple_with_long_deletion.prg.fa │ │ ├── match_update_simple_with_long_deletion.prg.gfa │ │ └── match_update_simple_with_long_deletion.update_DS.zip │ │ ├── nested_snps_seq_backgrounds_update │ │ ├── nested_snps_seq_backgrounds_update.prg.bin │ │ ├── nested_snps_seq_backgrounds_update.prg.fa │ │ ├── nested_snps_seq_backgrounds_update.prg.gfa │ │ └── nested_snps_seq_backgrounds_update.update_DS.zip │ │ ├── sample_example_update │ │ ├── sample_example_update.prg.bin.zip │ │ ├── sample_example_update.prg.fa │ │ ├── sample_example_update.prg.gfa.zip │ │ └── sample_example_update.update_DS.zip │ │ └── strict_insertions_and_deletions_update │ │ ├── strict_insertions_and_deletions_update.prg.bin │ │ ├── strict_insertions_and_deletions_update.prg.fa │ │ ├── strict_insertions_and_deletions_update.prg.gfa │ │ └── strict_insertions_and_deletions_update.update_DS.zip ├── test_from_msa.py └── test_update.py ├── test_helpers.py ├── test_output_type.py ├── test_prg_builder.py ├── test_recursion_tree.py ├── update ├── test_DenovoLocusInfo.py 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