#include "subcommand.hpp"
#include "../hash_map.hpp"
#include "../recombinator.hpp"
#include "../algorithms/extract_subchain.hpp"
#include <cmath>
#include <fstream>
#include <functional>
#include <iostream>
#include <thread>
#include <vector>
#include <unordered_map>
#include <getopt.h>
#include <omp.h>
#include <gbwtgraph/index.h>

Classes
struct	HaplotypesConfig

struct	ReferenceInterval

Namespaces
	haplotypes_defaults

Functions
size_t	haplotypes_defaults::threads ()

constexpr size_t	haplotypes_defaults::k ()

constexpr size_t	haplotypes_defaults::w ()

constexpr size_t	haplotypes_defaults::subchain_length ()

constexpr size_t	haplotypes_defaults::n ()

constexpr size_t	haplotypes_defaults::candidates ()

constexpr size_t	haplotypes_defaults::coverage ()

constexpr double	haplotypes_defaults::discount ()

constexpr double	haplotypes_defaults::adjustment ()

constexpr double	haplotypes_defaults::absent ()

constexpr double	haplotypes_defaults::badness ()

void	preprocess_graph (const gbwtgraph::GBZ &gbz, Haplotypes &haplotypes, HaplotypesConfig &config)

void	set_reference_samples (gbwtgraph::GBZ &gbz, const HaplotypesConfig &config)

void	sample_haplotypes (const gbwtgraph::GBZ &gbz, const Haplotypes &haplotypes, const HaplotypesConfig &config)

void	subchain_statistics (const gbwtgraph::GBZ &gbz, const Haplotypes &haplotypes, const HaplotypesConfig &config)

int	main_haplotypes (int argc, char **argv)

void	help_haplotypes (char **argv, bool developer_options)

void	validate_haplotypes (const Haplotypes &haplotypes, const gbwtgraph::GBWTGraph &graph, const gbwt::FastLocate &r_index, const HaplotypePartitioner::minimizer_index_type &minimizer_index, size_t expected_chains, HaplotypePartitioner::Verbosity verbosity)

bool	ends_with (const std::string &str, const std::string &suffix)

std::string	get_name (const std::string &graph_name, const std::string &extension)

size_t	threads_to_jobs (size_t threads)

void	validate_subgraph (const gbwtgraph::GBWTGraph &graph, const gbwtgraph::GBWTGraph &subgraph, HaplotypePartitioner::Verbosity verbosity)

gbwt::size_type	seq_for_chain (const gbwtgraph::GBZ &gbz, const Haplotypes &haplotypes, gbwt::size_type path_id, size_t chain_id)

std::pair< std::vector< ReferenceInterval >, size_t >	subchain_intervals (const gbwtgraph::GBZ &gbz, const Haplotypes &haplotypes, gbwt::size_type sequence_id, size_t chain_id)

gbwt::size_type	path_for_sample_contig (const gbwtgraph::GBZ &gbz, const std::string &sample_name, const std::string &contig_name)

void	validate_error (const std::string &header, const std::string &message)

template<typename T >
std::string	expected_got (T expected, T got)

template<typename T >
std::string	pair_to_string (std::pair< T, T > value)

void	validate_error_chain (size_t chain_id, const std::string &message)

void	validate_error_subchain (size_t chain_id, size_t subchain_id, const std::string &message)

void	validate_error_sequence (size_t chain_id, size_t subchain_id, size_t sequence_id, const std::string &message)

std::string	validate_unary_path (const HandleGraph &graph, handle_t from, handle_t to)

bool	trace_path (const gbwt::GBWT &index, const gbwt::FragmentMap &fragment_map, const hash_set< nid_t > &subchain_nodes, gbwt::size_type sequence_id, gbwt::node_type start, gbwt::size_type offset, gbwt::node_type end)

std::vector< std::string >	get_haplotype (const gbwtgraph::GBWTGraph &graph, const gbwt::FragmentMap &fragment_map, Haplotypes::sequence_type sequence, gbwt::node_type from, gbwt::node_type to, size_t k)

void	validate_chain (const Haplotypes::TopLevelChain &chain, const gbwtgraph::GBWTGraph &graph, const gbwt::FragmentMap &fragment_map, const gbwt::FastLocate &r_index, const HaplotypePartitioner::minimizer_index_type &minimizer_index, size_t chain_id, HaplotypePartitioner::Verbosity verbosity)

std::string	subchain_to_string (size_t chain_id, size_t subchain_id, const Haplotypes::Subchain &subchain)

void	validate_nodes (const gbwtgraph::GBWTGraph &graph, const gbwtgraph::GBWTGraph &subgraph)

void	validate_edges (const gbwtgraph::GBWTGraph &graph, const gbwtgraph::GBWTGraph &subgraph)

Variables
constexpr size_t	haplotypes_defaults::DEFAULT_MAX_THREADS = 16

Detailed Description

Defines the "vg haplotypes" subcommand, which samples haplotypes by kmer counts in the reads.

TODO: Tests for –linear-structure, –extra-fragments, and fragmented haplotypes.

Function Documentation

◆ ends_with()

bool ends_with	(	const std::string &	str,
		const std::string &	suffix
	)

◆ expected_got()

template<typename T >

std::string expected_got	(	T	expected,
		T	got
	)

◆ get_haplotype()

std::vector<std::string> get_haplotype	(	const gbwtgraph::GBWTGraph &	graph,
		const gbwt::FragmentMap &	fragment_map,
		Haplotypes::sequence_type	sequence,
		gbwt::node_type	from,
		gbwt::node_type	to,
		size_t	k
	)

◆ get_name()

std::string get_name	(	const std::string &	graph_name,
		const std::string &	extension
	)

◆ help_haplotypes()

void help_haplotypes	(	char **	argv,
		bool	developer_options
	)

◆ main_haplotypes()

int main_haplotypes	(	int	argc,
		char **	argv
	)

◆ pair_to_string()

template<typename T >

std::string pair_to_string ( std::pair< T, T > value )

◆ path_for_sample_contig()

gbwt::size_type path_for_sample_contig	(	const gbwtgraph::GBZ &	gbz,
		const std::string &	sample_name,
		const std::string &	contig_name
	)

◆ preprocess_graph()

void preprocess_graph	(	const gbwtgraph::GBZ &	gbz,
		Haplotypes &	haplotypes,
		HaplotypesConfig &	config
	)

◆ sample_haplotypes()

void sample_haplotypes	(	const gbwtgraph::GBZ &	gbz,
		const Haplotypes &	haplotypes,
		const HaplotypesConfig &	config
	)

◆ seq_for_chain()

gbwt::size_type seq_for_chain	(	const gbwtgraph::GBZ &	gbz,
		const Haplotypes &	haplotypes,
		gbwt::size_type	path_id,
		size_t	chain_id
	)

◆ set_reference_samples()

void set_reference_samples	(	gbwtgraph::GBZ &	gbz,
		const HaplotypesConfig &	config
	)

◆ subchain_intervals()

std::pair<std::vector<ReferenceInterval>, size_t> subchain_intervals	(	const gbwtgraph::GBZ &	gbz,
		const Haplotypes &	haplotypes,
		gbwt::size_type	sequence_id,
		size_t	chain_id
	)

◆ subchain_statistics()

void subchain_statistics	(	const gbwtgraph::GBZ &	gbz,
		const Haplotypes &	haplotypes,
		const HaplotypesConfig &	config
	)

◆ subchain_to_string()

std::string subchain_to_string	(	size_t	chain_id,
		size_t	subchain_id,
		const Haplotypes::Subchain &	subchain
	)

◆ threads_to_jobs()

size_t threads_to_jobs ( size_t threads )

◆ trace_path()

bool trace_path	(	const gbwt::GBWT &	index,
		const gbwt::FragmentMap &	fragment_map,
		const hash_set< nid_t > &	subchain_nodes,
		gbwt::size_type	sequence_id,
		gbwt::node_type	start,
		gbwt::size_type	offset,
		gbwt::node_type	end
	)

◆ validate_chain()

void validate_chain	(	const Haplotypes::TopLevelChain &	chain,
		const gbwtgraph::GBWTGraph &	graph,
		const gbwt::FragmentMap &	fragment_map,
		const gbwt::FastLocate &	r_index,
		const HaplotypePartitioner::minimizer_index_type &	minimizer_index,
		size_t	chain_id,
		HaplotypePartitioner::Verbosity	verbosity
	)

◆ validate_edges()

void validate_edges	(	const gbwtgraph::GBWTGraph &	graph,
		const gbwtgraph::GBWTGraph &	subgraph
	)

◆ validate_error()

void validate_error	(	const std::string &	header,
		const std::string &	message
	)

◆ validate_error_chain()

void validate_error_chain	(	size_t	chain_id,
		const std::string &	message
	)

◆ validate_error_sequence()

void validate_error_sequence	(	size_t	chain_id,
		size_t	subchain_id,
		size_t	sequence_id,
		const std::string &	message
	)

◆ validate_error_subchain()

void validate_error_subchain	(	size_t	chain_id,
		size_t	subchain_id,
		const std::string &	message
	)

◆ validate_haplotypes()

void validate_haplotypes	(	const Haplotypes &	haplotypes,
		const gbwtgraph::GBWTGraph &	graph,
		const gbwt::FastLocate &	r_index,
		const HaplotypePartitioner::minimizer_index_type &	minimizer_index,
		size_t	expected_chains,
		HaplotypePartitioner::Verbosity	verbosity
	)

◆ validate_nodes()

void validate_nodes	(	const gbwtgraph::GBWTGraph &	graph,
		const gbwtgraph::GBWTGraph &	subgraph
	)

◆ validate_subgraph()

void validate_subgraph	(	const gbwtgraph::GBWTGraph &	graph,
		const gbwtgraph::GBWTGraph &	subgraph,
		HaplotypePartitioner::Verbosity	verbosity
	)

◆ validate_unary_path()

std::string validate_unary_path	(	const HandleGraph &	graph,
		handle_t	from,
		handle_t	to
	)

Classes

Namespaces

Functions

Variables