HaplotypesConfig Struct Reference

Public Types
enum	OperatingMode {   mode_invalid, mode_sample_graph, mode_preprocess, mode_sample_haplotypes,   mode_map_variants, mode_extract, mode_classify }

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

Public Attributes
OperatingMode	mode = mode_invalid
Haplotypes::Verbosity	verbosity = Haplotypes::verbosity_silent
std::string	graph_name
std::string	gbz_output
std::string	haplotype_output
std::string	score_output
std::string	kmer_output
std::string	distance_name
std::string	r_index_name
std::string	haplotype_input
std::string	kmer_input
std::string	vcf_input
size_t	k = haplotypes_default_k()
size_t	w = haplotypes_default_w()
HaplotypePartitioner::Parameters	partitioner_parameters
Recombinator::Parameters	recombinator_parameters
std::string	contig_prefix
size_t	chain_id = std::numeric_limits<size_t>::max()
size_t	subchain_id = std::numeric_limits<size_t>::max()
size_t	threads = haplotypes_default_threads()
bool	validate = false

Member Enumeration Documentation

OperatingMode

enum HaplotypesConfig::OperatingMode

Enumerator
mode_invalid
mode_sample_graph
mode_preprocess
mode_sample_haplotypes
mode_map_variants
mode_extract
mode_classify

Constructor & Destructor Documentation

HaplotypesConfig()

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

Member Data Documentation

chain_id

size_t HaplotypesConfig::chain_id = std::numeric_limits<size_t>::max()

contig_prefix

std::string HaplotypesConfig::contig_prefix

distance_name

std::string HaplotypesConfig::distance_name

gbz_output

std::string HaplotypesConfig::gbz_output

graph_name

std::string HaplotypesConfig::graph_name

haplotype_input

std::string HaplotypesConfig::haplotype_input

haplotype_output

std::string HaplotypesConfig::haplotype_output

k

size_t HaplotypesConfig::k = haplotypes_default_k()

kmer_input

std::string HaplotypesConfig::kmer_input

kmer_output

std::string HaplotypesConfig::kmer_output

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

score_output

std::string HaplotypesConfig::score_output

subchain_id

size_t HaplotypesConfig::subchain_id = std::numeric_limits<size_t>::max()

threads

size_t HaplotypesConfig::threads = haplotypes_default_threads()

validate

bool HaplotypesConfig::validate = false

vcf_input

std::string HaplotypesConfig::vcf_input

verbosity

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

w

size_t HaplotypesConfig::w = haplotypes_default_w()

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

• src/subcommand/haplotypes_main.cpp