haplotypes_main.cpp File Reference

#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 <unordered_set>
#include <getopt.h>
#include <omp.h>
#include <gbwtgraph/index.h>

Classes
struct	HaplotypesConfig
struct	ReferenceInterval

Namespaces
namespace	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 ()
constexpr size_t	haplotypes_defaults::min_gref_len ()
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)
void	density_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 Logger &logger, 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)
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 Logger &logger, const gbwtgraph::GBWTGraph &graph, const gbwtgraph::GBWTGraph &subgraph, HaplotypePartitioner::Verbosity verbosity)
std::unordered_set< size_t >	resolve_chains_by_name (const gbwtgraph::GBZ &gbz, const Haplotypes &haplotypes, const std::vector< std::string > &names, const Logger &logger)
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 Logger &logger, const gbwtgraph::GBZ &gbz, const std::string &sample_name, const std::string &contig_name)
size_t	chain_for_path (const gbwtgraph::GBZ &gbz, const Haplotypes &haplotypes, gbwt::size_type path_id)
std::string	format_kmer_presence (size_t present, size_t total)
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 (const Logger &logger, size_t chain_id, const std::string &message)
void	validate_error_subchain (const Logger &logger, size_t chain_id, size_t subchain_id, const std::string &message)
void	validate_error_sequence (const Logger &logger, 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 vg::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 Logger &logger, 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 Logger &logger, const gbwtgraph::GBWTGraph &graph, const gbwtgraph::GBWTGraph &subgraph)
void	validate_edges (const Logger &logger, 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

chain_for_path()

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

density_statistics()

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

expected_got()

template<typename T>

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

format_kmer_presence()

std::string format_kmer_presence	(	size_t	present,
		size_t	total )

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 Logger &	logger,
		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 )

resolve_chains_by_name()

std::unordered_set< size_t > resolve_chains_by_name	(	const gbwtgraph::GBZ &	gbz,
		const Haplotypes &	haplotypes,
		const std::vector< std::string > &	names,
		const Logger &	logger )

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 vg::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 Logger &	logger,
		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 Logger &	logger,
		const gbwtgraph::GBWTGraph &	graph,
		const gbwtgraph::GBWTGraph &	subgraph )

validate_error_chain()

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

validate_error_sequence()

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

validate_error_subchain()

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

validate_haplotypes()

void validate_haplotypes	(	const Logger &	logger,
		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 Logger &	logger,
		const gbwtgraph::GBWTGraph &	graph,
		const gbwtgraph::GBWTGraph &	subgraph )

validate_subgraph()

void validate_subgraph	(	const Logger &	logger,
		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 )