vg
tools for working with variation graphs
Loading...
Searching...
No Matches
Public Types | Static Public Attributes | List of all members
vg::IndexingParameters Struct Reference

#include <index_registry.hpp>

Public Types

enum  MutableGraphImplementation { HashGraph , PackedGraph , VG }
enum  Verbosity { None = 0 , Basic = 1 , Debug = 2 }

Static Public Attributes

static MutableGraphImplementation mut_graph_impl = PackedGraph
static int max_node_size = 32
static int pruning_max_node_degree = 128
static int pruning_walk_length = 24
static int pruning_max_edge_count = 3
static int pruning_min_component_size = 33
static double pruning_walk_length_increase_factor = 1.5
static double pruning_max_node_degree_decrease_factor = 0.75
static int gcsa_initial_kmer_length = gcsa::Key::MAX_LENGTH
static int gcsa_doubling_steps = gcsa::ConstructionParameters::DOUBLING_STEPS
static int64_t gcsa_size_limit = 2ll * 1024ll * 1024ll * 1024ll * 1024ll
static int64_t gbwt_insert_batch_size = gbwt::DynamicGBWT::INSERT_BATCH_SIZE
static int gbwt_insert_batch_size_increase_factor = 10
static int gbwt_sampling_interval = gbwt::DynamicGBWT::SAMPLE_INTERVAL
static bool bidirectional_haplo_tx_gbwt = false
static string gff_feature_name = "exon"
static string gff_transcript_tag = "transcript_id"
static bool use_bounded_syncmers = false
static int short_read_minimizer_k = 29
static int short_read_minimizer_w = 11
static bool short_read_minimizer_W = false
static int long_read_minimizer_k = 31
static int long_read_minimizer_w = 50
static bool long_read_minimizer_W = true
static bool space_efficient_counting = false
static int minimizer_downweight_threshold = 500
static int minimizer_s = 18
static int path_cover_depth = gbwtgraph::PATH_COVER_DEFAULT_N
static int giraffe_gbwt_downsample = gbwtgraph::LOCAL_HAPLOTYPES_DEFAULT_N
static int downsample_context_length = gbwtgraph::PATH_COVER_DEFAULT_K
static int downsample_threshold = 3
static double max_memory_proportion = 0.75
static double thread_chunk_inflation_factor = 2.0
static Verbosity verbosity = IndexingParameters::Basic
static gbwtgraph::sample_name_set haplotype_sampling_reference_samples = {}
static size_t haplotype_sampling_num_haplotypes = Recombinator::NUM_CANDIDATES
static bool haplotype_sampling_diploid = true
static int haplotype_sampling_minimizer_k = 29
static int haplotype_sampling_minimizer_w = 11

Detailed Description

A struct namespace for global handling of parameters used by the IndexRegistry

Member Enumeration Documentation

◆ MutableGraphImplementation

enum vg::IndexingParameters::MutableGraphImplementation
Enumerator
HashGraph 
PackedGraph 
VG 

◆ Verbosity

enum vg::IndexingParameters::Verbosity
Enumerator
None 
Basic 
Debug 

Member Data Documentation

◆ bidirectional_haplo_tx_gbwt

bool vg::IndexingParameters::bidirectional_haplo_tx_gbwt = false
static

◆ downsample_context_length

int vg::IndexingParameters::downsample_context_length = gbwtgraph::PATH_COVER_DEFAULT_K
static

◆ downsample_threshold

int vg::IndexingParameters::downsample_threshold = 3
static

◆ gbwt_insert_batch_size

int64_t vg::IndexingParameters::gbwt_insert_batch_size = gbwt::DynamicGBWT::INSERT_BATCH_SIZE
static

◆ gbwt_insert_batch_size_increase_factor

int vg::IndexingParameters::gbwt_insert_batch_size_increase_factor = 10
static

◆ gbwt_sampling_interval

int vg::IndexingParameters::gbwt_sampling_interval = gbwt::DynamicGBWT::SAMPLE_INTERVAL
static

◆ gcsa_doubling_steps

int vg::IndexingParameters::gcsa_doubling_steps = gcsa::ConstructionParameters::DOUBLING_STEPS
static

◆ gcsa_initial_kmer_length

int vg::IndexingParameters::gcsa_initial_kmer_length = gcsa::Key::MAX_LENGTH
static

◆ gcsa_size_limit

int64_t vg::IndexingParameters::gcsa_size_limit = 2ll * 1024ll * 1024ll * 1024ll * 1024ll
static

◆ gff_feature_name

string vg::IndexingParameters::gff_feature_name = "exon"
static

◆ gff_transcript_tag

string vg::IndexingParameters::gff_transcript_tag = "transcript_id"
static

◆ giraffe_gbwt_downsample

int vg::IndexingParameters::giraffe_gbwt_downsample = gbwtgraph::LOCAL_HAPLOTYPES_DEFAULT_N
static

◆ haplotype_sampling_diploid

bool vg::IndexingParameters::haplotype_sampling_diploid = true
static

◆ haplotype_sampling_minimizer_k

int vg::IndexingParameters::haplotype_sampling_minimizer_k = 29
static

◆ haplotype_sampling_minimizer_w

int vg::IndexingParameters::haplotype_sampling_minimizer_w = 11
static

◆ haplotype_sampling_num_haplotypes

size_t vg::IndexingParameters::haplotype_sampling_num_haplotypes = Recombinator::NUM_CANDIDATES
static

◆ haplotype_sampling_reference_samples

gbwtgraph::sample_name_set vg::IndexingParameters::haplotype_sampling_reference_samples = {}
static

◆ long_read_minimizer_k

int vg::IndexingParameters::long_read_minimizer_k = 31
static

◆ long_read_minimizer_W

bool vg::IndexingParameters::long_read_minimizer_W = true
static

◆ long_read_minimizer_w

int vg::IndexingParameters::long_read_minimizer_w = 50
static

◆ max_memory_proportion

double vg::IndexingParameters::max_memory_proportion = 0.75
static

◆ max_node_size

int vg::IndexingParameters::max_node_size = 32
static

◆ minimizer_downweight_threshold

int vg::IndexingParameters::minimizer_downweight_threshold = 500
static

◆ minimizer_s

int vg::IndexingParameters::minimizer_s = 18
static

◆ mut_graph_impl

IndexingParameters::MutableGraphImplementation vg::IndexingParameters::mut_graph_impl = PackedGraph
static

◆ path_cover_depth

int vg::IndexingParameters::path_cover_depth = gbwtgraph::PATH_COVER_DEFAULT_N
static

◆ pruning_max_edge_count

int vg::IndexingParameters::pruning_max_edge_count = 3
static

◆ pruning_max_node_degree

int vg::IndexingParameters::pruning_max_node_degree = 128
static

◆ pruning_max_node_degree_decrease_factor

double vg::IndexingParameters::pruning_max_node_degree_decrease_factor = 0.75
static

◆ pruning_min_component_size

int vg::IndexingParameters::pruning_min_component_size = 33
static

◆ pruning_walk_length

int vg::IndexingParameters::pruning_walk_length = 24
static

◆ pruning_walk_length_increase_factor

double vg::IndexingParameters::pruning_walk_length_increase_factor = 1.5
static

◆ short_read_minimizer_k

int vg::IndexingParameters::short_read_minimizer_k = 29
static

◆ short_read_minimizer_W

bool vg::IndexingParameters::short_read_minimizer_W = false
static

◆ short_read_minimizer_w

int vg::IndexingParameters::short_read_minimizer_w = 11
static

◆ space_efficient_counting

bool vg::IndexingParameters::space_efficient_counting = false
static

◆ thread_chunk_inflation_factor

double vg::IndexingParameters::thread_chunk_inflation_factor = 2.0
static

◆ use_bounded_syncmers

bool vg::IndexingParameters::use_bounded_syncmers = false
static

◆ verbosity

IndexingParameters::Verbosity vg::IndexingParameters::verbosity = IndexingParameters::Basic
static
The documentation for this struct was generated from the following files:
Generated by   doxygen 1.17.0