HaplotypesConfig Struct Reference

Public Types
enum	OperatingMode {   mode_invalid , mode_sample_graph , mode_preprocess , mode_sample_haplotypes ,   mode_statistics , mode_density }

Public Member Functions
	HaplotypesConfig (int argc, char **argv, size_t max_threads)

Public Attributes
Logger	logger = Logger("vg haplotypes")
OperatingMode	mode = mode_invalid
Haplotypes::Verbosity	verbosity = Haplotypes::verbosity_silent
std::string	graph_name
std::string	gbz_output
std::string	haplotype_output
std::string	distance_name
std::string	r_index_name
std::string	haplotype_input
std::string	kmer_input
size_t	k = haplotypes_defaults::k()
size_t	w = haplotypes_defaults::w()
HaplotypePartitioner::Parameters	partitioner_parameters
Recombinator::Parameters	recombinator_parameters
gbwtgraph::sample_name_set	reference_samples
std::vector< std::string >	high_coverage_contigs
std::vector< std::string >	half_coverage_contigs
std::vector< std::string >	excluded_contigs
std::vector< std::string >	wrap_contigs
std::string	ref_sample
size_t	threads = haplotypes_defaults::threads()
bool	validate = false

Member Enumeration Documentation

OperatingMode

enum HaplotypesConfig::OperatingMode

Enumerator
mode_invalid
mode_sample_graph
mode_preprocess
mode_sample_haplotypes
mode_statistics
mode_density

Constructor & Destructor Documentation

HaplotypesConfig()

HaplotypesConfig::HaplotypesConfig	(	int	argc,
		char **	argv,
		size_t	max_threads )

Member Data Documentation

distance_name

std::string HaplotypesConfig::distance_name

excluded_contigs

std::vector<std::string> HaplotypesConfig::excluded_contigs

gbz_output

std::string HaplotypesConfig::gbz_output

graph_name

std::string HaplotypesConfig::graph_name

half_coverage_contigs

std::vector<std::string> HaplotypesConfig::half_coverage_contigs

haplotype_input

std::string HaplotypesConfig::haplotype_input

haplotype_output

std::string HaplotypesConfig::haplotype_output

high_coverage_contigs

std::vector<std::string> HaplotypesConfig::high_coverage_contigs

k

size_t HaplotypesConfig::k = haplotypes_defaults::k()

kmer_input

std::string HaplotypesConfig::kmer_input

logger

Logger HaplotypesConfig::logger = Logger("vg haplotypes")

mode

OperatingMode HaplotypesConfig::mode = mode_invalid

partitioner_parameters

HaplotypePartitioner::Parameters HaplotypesConfig::partitioner_parameters

r_index_name

std::string HaplotypesConfig::r_index_name

recombinator_parameters

Recombinator::Parameters HaplotypesConfig::recombinator_parameters

ref_sample

std::string HaplotypesConfig::ref_sample

reference_samples

gbwtgraph::sample_name_set HaplotypesConfig::reference_samples

threads

size_t HaplotypesConfig::threads = haplotypes_defaults::threads()

validate

bool HaplotypesConfig::validate = false

verbosity

Haplotypes::Verbosity HaplotypesConfig::verbosity = Haplotypes::verbosity_silent

w

size_t HaplotypesConfig::w = haplotypes_defaults::w()

wrap_contigs

std::vector<std::string> HaplotypesConfig::wrap_contigs

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

• src/subcommand/haplotypes_main.cpp