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	minimizer_k = 29
static int	minimizer_w = 11
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

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

max_memory_proportion

double vg::IndexingParameters::max_memory_proportion = 0.75

static

max_node_size

int vg::IndexingParameters::max_node_size = 32

static

minimizer_k

int vg::IndexingParameters::minimizer_k = 29

static

minimizer_s

int vg::IndexingParameters::minimizer_s = 18

static

minimizer_w

int vg::IndexingParameters::minimizer_w = 11

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

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

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The documentation for this struct was generated from the following files:

• src/index_registry.hpp
• src/index_registry.cpp