List of all items
Structs
- pca::PcaResult
- process::Args
- process::ConfigEntry
- process::FilteringStats
- process::MissingDataInfo
- process::OneBasedPosition
- process::QueryRegion
- process::SeqInfo
- process::Variant
- process::ZeroBasedHalfOpen
- process::ZeroBasedInclusive
- process::ZeroBasedPosition
- progress::ProgressTracker
- progress::StatusBox
- stats::DenseGenotypeMatrix
- stats::DensePopulationSummary
- stats::DxyHudsonResult
- stats::FstWcResults
- stats::HudsonFSTOutcome
- stats::PopulationContext
- stats::SiteDiversity
- stats::SiteFstHudson
- stats::SiteFstWc
- transcripts::CdsRegion
- transcripts::CdsSeq
- transcripts::TranscriptAnnotationCDS
Enums
- process::HaplotypeSide
- process::VcfError
- progress::LogLevel
- progress::ProcessingStage
- stats::FstEstimate
- stats::PopulationId
Functions
- parse::find_vcf_file
- parse::open_vcf_reader
- parse::parse_config_file
- parse::parse_gtf_file
- parse::parse_region
- parse::parse_regions_file
- parse::read_reference_sequence
- parse::validate_vcf_header
- pca::combine_chromosome_pca_results
- pca::compute_chromosome_pca
- pca::compute_chromosome_pca_from_dense
- pca::run_chromosome_pca_analysis
- pca::run_global_pca_analysis
- pca::write_chromosome_pca_to_file
- process::create_temp_dir
- process::display_seqinfo_entries
- process::get_haplotype_indices_for_group
- process::map_sample_names_to_indices
- process::process_config_entries
- process::process_variant
- process::process_variants
- process::process_vcf
- progress::create_spinner
- progress::create_vcf_progress
- progress::display_status_box
- progress::finish_all
- progress::finish_entry_progress
- progress::finish_step_progress
- progress::finish_variant_progress
- progress::init_entry_progress
- progress::init_global_progress
- progress::init_step_progress
- progress::init_variant_progress
- progress::log
- progress::set_stage
- progress::update_entry_progress
- progress::update_global_progress
- progress::update_step_progress
- progress::update_variant_progress
- stats::aggregate_hudson_from_sites
- stats::build_dense_population_summary
- stats::calculate_adjusted_sequence_length
- stats::calculate_d_xy_hudson
- stats::calculate_fst_wc_csv_populations
- stats::calculate_fst_wc_haplotype_groups
- stats::calculate_hudson_fst_for_pair
- stats::calculate_hudson_fst_for_pair_with_sites
- stats::calculate_hudson_fst_per_site
- stats::calculate_inversion_allele_frequency
- stats::calculate_pairwise_differences
- stats::calculate_per_site_diversity
- stats::calculate_pi
- stats::calculate_pi_for_population
- stats::calculate_watterson_theta
- stats::compute_hudson_fst_outcome
- stats::core_sample_id
- stats::count_segregating_sites
- stats::count_segregating_sites_for_population
- stats::extract_wc_fst_components
- stats::harmonic
- stats::parse_population_csv
- transcripts::apply_variants_to_transcripts
- transcripts::filter_and_log_transcripts
- transcripts::generate_batch_statistics
- transcripts::initialize_hap_sequences
- transcripts::make_sequences
- transcripts::prepare_to_write_cds
- transcripts::write_phylip_file