GBWTConfig Struct Reference

Public Types
enum	build_mode {   build_none , build_vcf , build_gfa , build_paths ,   build_alignments , build_gbz }
enum	merge_mode { merge_none , merge_insert , merge_fast , merge_parallel }
enum	path_cover_mode { path_cover_none , path_cover_augment , path_cover_local , path_cover_greedy }

Public Member Functions
	GBWTConfig ()
gbwtgraph::PathCoverParameters	path_cover_parameters () const

Static Public Member Functions
static size_t	default_build_jobs ()
static constexpr size_t	default_num_paths ()
static constexpr size_t	default_num_paths_local ()
static constexpr size_t	default_context_length ()
static size_t	default_merge_jobs ()

Public Attributes
Logger	logger = Logger("vg gbwt")
bool	produces_one_gbwt = false
build_mode	build = build_none
merge_mode	merge = merge_none
path_cover_mode	path_cover = path_cover_none
bool	metadata_mode = false
bool	path_mode = false
HaplotypeIndexer	haplotype_indexer
bool	gam_format = false
bool	inputs_as_jobs = false
bool	parse_only = false
size_t	build_jobs = default_build_jobs()
gbwtgraph::GFAParsingParameters	gfa_parameters = get_best_gbwtgraph_gfa_parsing_parameters()
gbwt::MergeParameters	merge_parameters
bool	set_pggname = false
std::string	supergraph_filename
bool	unset_pggname = false
std::uint32_t	gbz_version = 0
bool	show_progress = false
bool	count_paths = false
bool	metadata = false
bool	contigs = false
bool	haplotypes = false
bool	samples = false
bool	list_names = false
bool	path_names = false
bool	tags = false
bool	include_named_paths = false
size_t	num_paths = default_num_paths()
size_t	context_length = default_context_length()
bool	num_paths_set = false
size_t	search_threads = omp_get_max_threads()
std::vector< std::string >	input_filenames
std::string	gbwt_name
std::string	graph_name
std::string	gbwtgraph_name
std::string	gbwt_output
std::string	path_output
std::string	graph_output
std::string	segment_translation
std::string	r_index_name
std::set< std::string >	to_remove
std::map< std::string, std::string >	tags_to_set
std::unordered_set< std::string >	wrap_contigs

Member Enumeration Documentation

build_mode

enum GBWTConfig::build_mode

Enumerator
build_none
build_vcf
build_gfa
build_paths
build_alignments
build_gbz

merge_mode

enum GBWTConfig::merge_mode

Enumerator
merge_none
merge_insert
merge_fast
merge_parallel

path_cover_mode

enum GBWTConfig::path_cover_mode

Enumerator
path_cover_none
path_cover_augment
path_cover_local
path_cover_greedy

Constructor & Destructor Documentation

GBWTConfig()

GBWTConfig::GBWTConfig ( )

inline

Member Function Documentation

default_build_jobs()

size_t GBWTConfig::default_build_jobs ( )

inlinestatic

default_context_length()

constexpr size_t GBWTConfig::default_context_length ( )

inlinestaticconstexpr

default_merge_jobs()

size_t GBWTConfig::default_merge_jobs ( )

inlinestatic

default_num_paths()

constexpr size_t GBWTConfig::default_num_paths ( )

inlinestaticconstexpr

default_num_paths_local()

constexpr size_t GBWTConfig::default_num_paths_local ( )

inlinestaticconstexpr

path_cover_parameters()

gbwtgraph::PathCoverParameters GBWTConfig::path_cover_parameters ( ) const

inline

Member Data Documentation

build

build_mode GBWTConfig::build = build_none

build_jobs

size_t GBWTConfig::build_jobs = default_build_jobs()

context_length

size_t GBWTConfig::context_length = default_context_length()

contigs

bool GBWTConfig::contigs = false

count_paths

bool GBWTConfig::count_paths = false

gam_format

bool GBWTConfig::gam_format = false

gbwt_name

std::string GBWTConfig::gbwt_name

gbwt_output

std::string GBWTConfig::gbwt_output

gbwtgraph_name

std::string GBWTConfig::gbwtgraph_name

gbz_version

std::uint32_t GBWTConfig::gbz_version = 0

gfa_parameters

gbwtgraph::GFAParsingParameters GBWTConfig::gfa_parameters = get_best_gbwtgraph_gfa_parsing_parameters()

graph_name

std::string GBWTConfig::graph_name

graph_output

std::string GBWTConfig::graph_output

haplotype_indexer

HaplotypeIndexer GBWTConfig::haplotype_indexer

haplotypes

bool GBWTConfig::haplotypes = false

include_named_paths

bool GBWTConfig::include_named_paths = false

input_filenames

std::vector<std::string> GBWTConfig::input_filenames

inputs_as_jobs

bool GBWTConfig::inputs_as_jobs = false

list_names

bool GBWTConfig::list_names = false

logger

Logger GBWTConfig::logger = Logger("vg gbwt")

merge

merge_mode GBWTConfig::merge = merge_none

merge_parameters

gbwt::MergeParameters GBWTConfig::merge_parameters

metadata

bool GBWTConfig::metadata = false

metadata_mode

bool GBWTConfig::metadata_mode = false

num_paths

size_t GBWTConfig::num_paths = default_num_paths()

num_paths_set

bool GBWTConfig::num_paths_set = false

parse_only

bool GBWTConfig::parse_only = false

path_cover

path_cover_mode GBWTConfig::path_cover = path_cover_none

path_mode

bool GBWTConfig::path_mode = false

path_names

bool GBWTConfig::path_names = false

path_output

std::string GBWTConfig::path_output

produces_one_gbwt

bool GBWTConfig::produces_one_gbwt = false

r_index_name

std::string GBWTConfig::r_index_name

samples

bool GBWTConfig::samples = false

search_threads

size_t GBWTConfig::search_threads = omp_get_max_threads()

segment_translation

std::string GBWTConfig::segment_translation

set_pggname

bool GBWTConfig::set_pggname = false

show_progress

bool GBWTConfig::show_progress = false

supergraph_filename

std::string GBWTConfig::supergraph_filename

tags

bool GBWTConfig::tags = false

tags_to_set

std::map<std::string, std::string> GBWTConfig::tags_to_set

to_remove

std::set<std::string> GBWTConfig::to_remove

unset_pggname

bool GBWTConfig::unset_pggname = false

wrap_contigs

std::unordered_set<std::string> GBWTConfig::wrap_contigs

---

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

• src/subcommand/gbwt_main.cpp