├── .clang-format ├── .codecov.yml ├── .gitattributes ├── .gitignore ├── .gitmodules ├── .travis.yml ├── CMakeLists.txt ├── LICENSE ├── README.md ├── docs ├── classification.md ├── custom_databases.md ├── default_databases.md ├── index.md ├── outputfiles.md ├── reports.md ├── start.md ├── table.md └── tutorials.md ├── ganon ├── mkdocs.yml ├── scripts └── ganon-get-seq-info.sh ├── setup.cfg ├── setup.py ├── src ├── CMakeLists.txt ├── __init__.py ├── defaults │ └── defaults.hpp.in ├── ganon-build │ ├── CommandLineParser.cpp │ ├── GanonBuild.cpp │ ├── include │ │ └── ganon-build │ │ │ ├── CommandLineParser.hpp │ │ │ ├── Config.hpp │ │ │ └── GanonBuild.hpp │ └── main.cpp ├── ganon-classify │ ├── CommandLineParser.cpp │ ├── GanonClassify.cpp │ ├── include │ │ └── ganon-classify │ │ │ ├── CommandLineParser.hpp │ │ │ ├── Config.hpp │ │ │ ├── GanonClassify.hpp │ │ │ ├── LICENSE_hierarchical_interleaved_bloom_filter.md │ │ │ └── hierarchical_interleaved_bloom_filter.hpp │ └── main.cpp ├── ganon │ ├── __init__.py │ ├── build_update.py │ ├── classify.py │ ├── config.py │ ├── ganon.py │ ├── reassign.py │ ├── report.py │ ├── table.py │ ├── tax_util.py │ └── util.py └── utils │ └── include │ └── utils │ ├── IBFConfig.hpp │ ├── LCA.hpp │ ├── SafeQueue.hpp │ ├── StopClock.hpp │ ├── adjust_seed.hpp │ └── dna4_traits.hpp └── tests ├── CMakeLists.txt ├── aux └── Aux.hpp ├── ganon-build ├── GanonBuild.test.cpp └── data │ ├── SEQ0.fna.gz │ ├── SEQ1.fna.gz │ ├── SEQ10.fna.gz │ ├── SEQ11.fna.gz │ ├── SEQ12.fna.gz │ ├── SEQ13.fna.gz │ ├── SEQ14.fna.gz │ ├── SEQ15.fna.gz │ ├── SEQ16.fna.gz │ ├── SEQ17.fna.gz │ ├── SEQ18.fna.gz │ ├── SEQ19.fna.gz │ ├── SEQ2.fna.gz │ ├── SEQ20.fna.gz │ ├── SEQ21.fna.gz │ ├── SEQ22.fna.gz │ ├── SEQ23.fna.gz │ ├── SEQ24.fna.gz │ ├── SEQ3.fna.gz │ ├── SEQ4.fna.gz │ ├── SEQ5.fna.gz │ ├── SEQ6.fna.gz │ ├── SEQ7.fna.gz │ ├── SEQ8.fna.gz │ ├── SEQ9.fna.gz │ └── mode_input.tsv ├── ganon-classify └── GanonClassify.test.cpp ├── ganon ├── data │ ├── build-custom │ │ ├── ar53_metadata.tsv.gz │ │ ├── ar53_taxonomy.tsv.gz │ │ ├── assembly_summary.txt │ │ ├── assembly_summary_empty.txt │ │ ├── bac120_metadata.tsv.gz │ │ ├── bac120_taxonomy.tsv.gz │ │ ├── files │ │ │ ├── GCA_000147015.1_ASM14701v1_genomic.fna.gz │ │ │ ├── GCA_002254805.1_ASM225480v1_genomic.fna.gz │ │ │ ├── GCF_004296495.1_ASM429649v1_genomic.fna.gz │ │ │ ├── GCF_009617975.1_ASM961797v1_genomic.fna.gz │ │ │ └── more │ │ │ │ ├── GCA_015134435.1_ASM1513443v1_genomic.fna.gz │ │ │ │ ├── GCA_018304365.1_ASM1830436v1_genomic.fna.gz │ │ │ │ ├── GCF_002214165.1_ASM221416v1_genomic.fna.gz │ │ │ │ └── GCF_017656055.1_ASM1765605v1_genomic.fna.gz │ │ ├── filter_files.sh │ │ ├── nucl_gb.accession2taxid.gz │ │ ├── remote │ │ │ ├── genomes │ │ │ │ ├── ASSEMBLY_REPORTS │ │ │ │ │ └── species_genome_size.txt.gz │ │ │ │ ├── genbank │ │ │ │ │ └── assembly_summary_genbank.txt │ │ │ │ └── refseq │ │ │ │ │ └── assembly_summary_refseq.txt │ │ │ └── pub │ │ │ │ └── taxonomy │ │ │ │ └── accession2taxid │ │ │ │ └── nucl_gb.accession2taxid.gz │ │ ├── species_genome_size.txt.gz │ │ └── taxdump.tar.gz │ ├── build │ │ ├── genomes │ │ │ ├── all │ │ │ │ └── GCA │ │ │ │ │ ├── 000 │ │ │ │ │ └── 147 │ │ │ │ │ │ └── 015 │ │ │ │ │ │ └── GCA_000147015.1_ASM14701v1 │ │ │ │ │ │ └── GCA_000147015.1_ASM14701v1_genomic.fna.gz │ │ │ │ │ ├── 002 │ │ │ │ │ └── 254 │ │ │ │ │ │ └── 805 │ │ │ │ │ │ └── GCA_002254805.1_ASM225480v1 │ │ │ │ │ │ └── GCA_002254805.1_ASM225480v1_genomic.fna.gz │ │ │ │ │ └── 004 │ │ │ │ │ └── 132 │ │ │ │ │ └── 065 │ │ │ │ │ └── GCA_004132065.1_ASM413206v1 │ │ │ │ │ └── GCA_004132065.1_ASM413206v1_genomic.fna.gz │ │ │ └── genbank │ │ │ │ ├── archaea │ │ │ │ ├── assembly_summary.txt │ │ │ │ └── assembly_summary_historical.txt │ │ │ │ ├── assembly_summary_genbank.txt │ │ │ │ ├── assembly_summary_genbank_historical.txt │ │ │ │ ├── bacteria │ │ │ │ ├── assembly_summary.txt │ │ │ │ └── assembly_summary_historical.txt │ │ │ │ └── viral │ │ │ │ ├── assembly_summary.txt │ │ │ │ └── assembly_summary_historical.txt │ │ ├── pub │ │ │ └── taxonomy │ │ │ │ └── new_taxdump │ │ │ │ ├── new_taxdump.tar.gz │ │ │ │ └── new_taxdump.tar.gz.md5 │ │ └── releases │ │ │ └── latest │ │ │ ├── MD5SUM.txt │ │ │ ├── ar53_taxonomy.tsv.gz │ │ │ └── bac120_taxonomy.tsv.gz │ ├── classify │ │ ├── sim.1.fq.gz │ │ └── sim.2.fq.gz │ ├── download_test_set_build.sh │ ├── reassign │ │ └── sim.fq.gz │ └── table │ │ ├── report_matches1.tre │ │ ├── report_matches2.tre │ │ ├── report_matches3.tre │ │ ├── report_reads1.tre │ │ ├── report_reads2.tre │ │ └── report_reads3.tre ├── integration │ ├── test_build.py │ ├── test_build_custom.py │ ├── test_classify.py │ ├── test_reassign.py │ ├── test_report.py │ ├── test_table.py │ └── test_update.py ├── integration_online │ ├── test_build_custom.py │ └── test_report.py └── utils.py ├── setup └── Catch2.setup.cpp └── utils ├── LCA.test.cpp ├── SafeQueue.test.cpp └── data └── lca ├── ncbi.tax └── tree.tax /.clang-format: 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