├── .clang-format ├── .dockerignore ├── .gitignore ├── .pre-commit-config.yaml ├── .travis.yml ├── CHANGELOG.md ├── CMakeLists.txt ├── CONTRIBUTING.md ├── LICENCE ├── MANIFEST.in ├── README.md ├── ci ├── docker │ ├── Dockerfile │ ├── Dockerfile_portable_binary │ └── purge.sh ├── install_deps.sh ├── singularity │ └── gramtools.def └── travis_build.sh ├── conanfile.txt ├── doc └── Doxyfile.in ├── gramtools ├── __init__.py ├── commands │ ├── __init__.py │ ├── build │ │ ├── __init__.py │ │ ├── build.py │ │ ├── command_setup.py │ │ ├── from_msas.py │ │ ├── from_vcfs.py │ │ └── vcf_to_prg_string.py │ ├── common.py │ ├── discover │ │ ├── __init__.py │ │ ├── command_setup.py │ │ └── discover.py │ ├── genotype │ │ ├── __init__.py │ │ ├── command_setup.py │ │ ├── genotype.py │ │ ├── seq_region_map.py │ │ └── utils.py │ ├── paths.py │ ├── report.py │ └── simulate │ │ ├── __init__.py │ │ └── simulate.py ├── gramtools_main.py ├── tests │ ├── __init__.py │ ├── build_command │ │ ├── __init__.py │ │ ├── test_from_msas.py │ │ ├── test_from_msas_integration_tests.py │ │ └── test_vcf_to_prg_string.py │ ├── common.py │ ├── discover │ │ ├── __init__.py │ │ ├── test_discover_integration_tests.py │ │ └── test_discover_unit_tests.py │ ├── genotype │ │ ├── test_genotype_integration_tests.py │ │ └── test_seq_region_map.py │ ├── integration_test_data │ │ ├── IT1 │ │ │ ├── prg.bin │ │ │ ├── reads.fastq │ │ │ └── ref.fa │ │ ├── IT2 │ │ │ ├── prg.bin │ │ │ ├── reads.fastq │ │ │ └── ref.fa │ │ ├── IT3 │ │ │ ├── prg.bin │ │ │ ├── reads.fastq │ │ │ └── ref.fa │ │ ├── IT4 │ │ │ ├── geno.vcf.gz │ │ │ ├── more_reads.fq.gz │ │ │ ├── pers_ref.fa │ │ │ ├── pers_ref_with_var.fa │ │ │ └── reads.fq.gz │ │ ├── from_msas │ │ │ ├── chrom_sizes.tsv │ │ │ ├── ref.fa │ │ │ ├── reg1.msa │ │ │ ├── reg2.bin │ │ │ └── to_build.bed │ │ └── vcf_to_prg_string │ │ │ ├── bad_header_complex_variant.ref.fa │ │ │ ├── bad_header_complex_variant.vcf │ │ │ ├── two_adjacent_snps_two_alts.prg │ │ │ ├── two_adjacent_snps_two_alts.ref.fa │ │ │ └── two_adjacent_snps_two_alts.vcf │ ├── mocks.py │ └── simulate │ │ └── test_simulate_integration_tests.py └── version │ ├── Makefile │ ├── __init__.py │ ├── package_version.py │ └── report.py ├── libgramtools ├── CMakeLists.txt ├── cmake_modules │ └── CodeCoverage.cmake ├── include │ ├── build │ │ ├── build.hpp │ │ ├── check_ref.hpp │ │ ├── kmer_index │ │ │ ├── build.hpp │ │ │ ├── dump.hpp │ │ │ ├── kmer_index_types.hpp │ │ │ ├── kmers.hpp │ │ │ ├── load.hpp │ │ │ └── masks.hpp │ │ └── parameters.hpp │ ├── common │ │ ├── data_types.hpp │ │ ├── file_read.hpp │ │ ├── parameters.hpp │ │ ├── random.hpp │ │ ├── timer_report.hpp │ │ └── utils.hpp │ ├── genotype │ │ ├── genotype.hpp │ │ ├── infer │ │ │ ├── allele_extracter.hpp │ │ │ ├── interfaces.hpp │ │ │ ├── level_genotyping │ │ │ │ ├── model.hpp │ │ │ │ ├── probabilities.hpp │ │ │ │ ├── runner.hpp │ │ │ │ └── site.hpp │ │ │ ├── output_specs │ │ │ │ ├── fields.hpp │ │ │ │ ├── json_prg_spec.hpp │ │ │ │ ├── json_site_spec.hpp │ │ │ │ ├── make_json.hpp │ │ │ │ ├── make_vcf.hpp │ │ │ │ └── segment_tracker.hpp │ │ │ ├── personalised_reference.hpp │ │ │ └── types.hpp │ │ ├── parameters.hpp │ │ ├── quasimap │ │ │ ├── coverage │ │ │ │ ├── allele_base.hpp │ │ │ │ ├── allele_sum.hpp │ │ │ │ ├── coverage_common.hpp │ │ │ │ ├── grouped_allele_counts.hpp │ │ │ │ └── types.hpp │ │ │ ├── quasimap.hpp │ │ │ └── search │ │ │ │ ├── BWT_search.hpp │ │ │ │ ├── encapsulated_search.hpp │ │ │ │ ├── types.hpp │ │ │ │ └── vBWT_jump.hpp │ │ └── read_stats.hpp │ ├── prg │ │ ├── coverage_graph.hpp │ │ ├── linearised_prg.hpp │ │ ├── make_data_structures.hpp │ │ ├── prg_info.hpp │ │ └── types.hpp │ ├── sequence_read │ │ ├── seq_file.h │ │ ├── seqread.hpp │ │ └── stream_buffer.h │ └── simulate │ │ ├── induce_genotypes.hpp │ │ ├── parameters.hpp │ │ └── simulate.hpp ├── lib │ ├── GCP │ │ └── GCP.h │ ├── boost.cmake │ ├── gzstream │ │ ├── gzstream.C │ │ └── gzstream.h │ ├── htslib.cmake │ └── sdsl.cmake ├── src │ ├── build │ │ ├── build.cpp │ │ ├── check_ref.cpp │ │ ├── kmer_index │ │ │ ├── build.cpp │ │ │ ├── dump.cpp │ │ │ ├── kmers.cpp │ │ │ ├── load.cpp │ │ │ └── masks.cpp │ │ └── parameters.cpp │ ├── common │ │ ├── file_read.cpp │ │ ├── parameters.cpp │ │ ├── random.cpp │ │ ├── timer_report.cpp │ │ └── utils.cpp │ ├── genotype │ │ ├── genotype.cpp │ │ ├── infer │ │ │ ├── allele_extracter.cpp │ │ │ ├── interfaces.cpp │ │ │ ├── level_genotyping │ │ │ │ ├── model.cpp │ │ │ │ ├── probabilities.cpp │ │ │ │ ├── runner.cpp │ │ │ │ └── site.cpp │ │ │ ├── output_specs │ │ │ │ ├── json_prg_spec.cpp │ │ │ │ ├── json_site_spec.cpp │ │ │ │ ├── make_json.cpp │ │ │ │ └── make_vcf.cpp │ │ │ └── personalised_reference.cpp │ │ ├── parameters.cpp │ │ ├── quasimap │ │ │ ├── coverage │ │ │ │ ├── allele_base.cpp │ │ │ │ ├── allele_sum.cpp │ │ │ │ ├── coverage_common.cpp │ │ │ │ └── grouped_allele_counts.cpp │ │ │ ├── quasimap.cpp │ │ │ └── search │ │ │ │ ├── BWT_search.cpp │ │ │ │ ├── encapsulated_search.cpp │ │ │ │ └── vBWT_jump.cpp │ │ └── read_stats.cpp │ ├── main.cpp │ ├── prg │ │ ├── coverage_graph.cpp │ │ ├── linearised_prg.cpp │ │ ├── make_data_structures.cpp │ │ └── prg_info.cpp │ └── simulate │ │ ├── induce_genotypes.cpp │ │ ├── parameters.cpp │ │ └── simulate.cpp ├── submods │ ├── CMakeLists.txt │ ├── README.md │ ├── combine_jvcfs.cpp │ ├── encode_prg.cpp │ ├── print_fm_index.cpp │ ├── submod_resources.cpp │ ├── submod_resources.hpp │ └── visualise_prg.cpp └── tests │ ├── CMakeLists.txt │ ├── build │ ├── kmer_index │ │ ├── test_build.cpp │ │ ├── test_dump_and_load.cpp │ │ ├── test_kmers.cpp │ │ └── test_masks.cpp │ └── test_check_ref.cpp │ ├── genotype │ ├── infer │ │ ├── level_genotyping │ │ │ ├── test_model.cpp │ │ │ ├── test_probabilities.cpp │ │ │ └── test_runner.cpp │ │ ├── mocks.hpp │ │ ├── test_allele_extracter.cpp │ │ ├── test_interfaces.cpp │ │ ├── test_json_spec.cpp │ │ ├── test_personalised_reference.cpp │ │ ├── test_segment_tracker.cpp │ │ └── test_types.cpp │ ├── 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