List of all items
Structs
- graphs::matrix_graph::MatrixGraph
- graphs::matrix_graph::Point
- libs::args::ConciseArgs
- libs::args::GraphArgs
- libs::args::StandardArgs
- libs::clap::Arguments
- libs::clap::LogAndVerbosity
- libs::stats::Difference
- libs::stats::Summary
- libs::structs::Coord
- libs::structs::HapVariant
- libs::structs::PhasedMatrix
- libs::structs::ReadMetadata
- subcommands::bhst::Hst
- subcommands::bhst::Metadata
- subcommands::bhst::Node
- subcommands::compare_haplotypes::CompareHaplotype
- subcommands::compare_haplotypes::HaplotypeAligner
- subcommands::haplotype_to_vcf::VcfRow
- subcommands::list_markers::HstMetadata
Enums
- libs::args::Selection
- libs::args::SortOption
- libs::clap::SubCommand
- libs::error::HaptkError
- libs::structs::Ploidy
- subcommands::bhst::HstType
Traits
Functions
- graphs::matrix_graph::determine_line_color
- libs::clap::get_styles
- libs::clap::init_tracing
- libs::clap::run_args
- libs::clap::run_cmd
- libs::io::append_ext
- libs::io::check_recombination_file_matches_contig
- libs::io::filter_out_non_vcf_sample_names
- libs::io::get_csv_reader
- libs::io::get_csv_writer
- libs::io::get_htslib_bcf_contigs
- libs::io::get_htslib_contig_len
- libs::io::get_input
- libs::io::get_output
- libs::io::get_strict_tsv_writer
- libs::io::get_tsv_reader
- libs::io::get_vcf_writer
- libs::io::open_csv_writer
- libs::io::open_strict_tsv_writer
- libs::io::push_to_output
- libs::io::read_coords_file
- libs::io::read_haplotype_file
- libs::io::read_lines
- libs::io::read_multiple_sample_ids
- libs::io::read_recombination_file
- libs::io::read_sample_ids
- libs::io::read_tabix
- libs::io::return_double_extension_filetype
- libs::io::spawn_csv_collector
- libs::io::write_haplotype
- libs::read_vcf::filter_samples
- libs::read_vcf::get_reader
- libs::read_vcf::get_sample_names
- libs::read_vcf::get_samples
- libs::read_vcf::read_shard_of_vcf
- libs::read_vcf::read_vcf_to_matrix
- libs::read_vcf::read_vcf_to_matrix_by_indexes
- libs::stats::two_tail_mann_whitney_u_test_no_corr
- libs::stats::two_tail_welch_t_test
- libs::stats::two_tail_welch_t_test2
- libs::structs::is_contradictory_by_idx
- libs::utils::centromeres_hg38
- libs::utils::parse_coords
- libs::utils::parse_snp_coord
- libs::utils::precision_f64
- libs::utils::strip_prefix
- subcommands::bhst::calculate_block_len
- subcommands::bhst::find_coord_list
- subcommands::bhst::find_highest_stop
- subcommands::bhst::find_lowest_start
- subcommands::bhst::find_majority_nodes
- subcommands::bhst::find_mbah
- subcommands::bhst::find_shared_haplotype
- subcommands::bhst::initiate_hst
- subcommands::bhst::insert_nodes_to_bhst
- subcommands::bhst::read_hst_file
- subcommands::bhst::read_vcf_with_selections
- subcommands::bhst::write_hst_file
- subcommands::check_for_haplotype::identical_haplotype_count
- subcommands::compare_haplotypes::get_csv_reader
- subcommands::compare_haplotypes::read_haplotype_file
- subcommands::compare_haplotypes::run
- subcommands::compare_to_haplotype::find_shared_haplotype_ranges
- subcommands::compare_to_haplotype::print_ranges_to_csv
- subcommands::compare_to_haplotype::range_length_avg
- subcommands::compare_to_haplotype::range_length_median
- subcommands::compare_to_haplotype::transform_gt_matrix_to_match_matrix
- subcommands::compare_to_hst::no_contradictory_genotypes_in_ht
- subcommands::compare_to_hst::populate_imported_hst
- subcommands::compare_to_hst::recursive_haplotype_comparison
- subcommands::compare_to_hst::remove_non_max_leaf_nodes
- subcommands::fasta_to_haplotype::parse_seq_name
- subcommands::fasta_to_haplotype::run
- subcommands::haplotype_to_vcf::header
- subcommands::haplotype_to_vcf::run
- subcommands::list_haplotypes::get_unique_haplotypes_map
- subcommands::list_haplotypes::write_genotype_file
- subcommands::list_haplotypes::write_haplotype_file
- subcommands::list_markers::read_hst_coords
- subcommands::list_samples::get_sample_names
- subcommands::list_samples::read_hst_samples
- subcommands::mrca::correlated
- subcommands::mrca::get_sums
- subcommands::mrca::independent
- subcommands::mrca::mrca_gamma_method
- subcommands::mrca::mrca_independent
- subcommands::uhst::combine_node_haplotypes
- subcommands::uhst::insert_nodes_to_uhst