convert_main.cpp File Reference

#include "subcommand.hpp"
#include "../vg.hpp"
#include "../utility.hpp"
#include "xg.hpp"
#include "../algorithms/gfa_to_handle.hpp"
#include "../algorithms/find_gbwtgraph.hpp"
#include "../io/save_handle_graph.hpp"
#include "../gfa.hpp"
#include "../gbwt_helper.hpp"
#include "../gbwtgraph_helper.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <vg/io/alignment_emitter.hpp>
#include "bdsg/packed_graph.hpp"
#include "bdsg/hash_graph.hpp"
#include <gbwtgraph/gbz.h>
#include <gbwtgraph/gfa.h>
#include <unistd.h>
#include <getopt.h>

Enumerations
enum	input_type {   input_handlegraph, input_gam, input_gaf, input_gfa,   input_gbwtgraph }
enum	algorithm_type { algorithm_auto, algorithm_vg, algorithm_gbwtgraph }

Functions
void	help_convert (char **argv)
void	no_multiple_inputs (input_type input)
void	graph_to_xg_adjusting_paths (const PathHandleGraph *input, xg::XG *output, const std::unordered_set< std::string > &ref_samples, const std::string &hap_locus, const std::string &new_sample, bool drop_haplotypes)
void	add_and_adjust_paths (const PathHandleGraph *input, MutablePathHandleGraph *output, const std::unordered_set< std::string > &ref_samples, const std::string &hap_locus, const std::string &new_sample, bool drop_haplotypes)
int	main_convert (int argc, char **argv)
std::unordered_map< std::string, std::unordered_set< int64_t > >	check_duplicate_path_names (const PathHandleGraph *input, const std::unordered_set< std::string > &ref_samples)

Variables
const input_type	INPUT_DEFAULT = input_handlegraph
const algorithm_type	ALGORITHM_DEFAULT = algorithm_auto

Enumeration Type Documentation

algorithm_type

enum algorithm_type

Enumerator
algorithm_auto
algorithm_vg
algorithm_gbwtgraph

input_type

enum input_type

Enumerator
input_handlegraph
input_gam
input_gaf
input_gfa
input_gbwtgraph

Function Documentation

add_and_adjust_paths()

void add_and_adjust_paths	(	const PathHandleGraph *	input,
		MutablePathHandleGraph *	output,
		const std::unordered_set< std::string > &	ref_samples,
		const std::string &	hap_locus,
		const std::string &	new_sample,
		bool	drop_haplotypes
	)

check_duplicate_path_names()

std::unordered_map<std::string, std::unordered_set<int64_t> > check_duplicate_path_names	(	const PathHandleGraph *	input,
		const std::unordered_set< std::string > &	ref_samples
	)

Check to make sure the haplotype paths with sample names in the given set have no more than one phase block per sample/haplotype/contig combination. Also return a map from sample name to set of observed haplotype numbers (so we can include them in reference-sense paths only if needed).

graph_to_xg_adjusting_paths()

void graph_to_xg_adjusting_paths	(	const PathHandleGraph *	input,
		xg::XG *	output,
		const std::unordered_set< std::string > &	ref_samples,
		const std::string &	hap_locus,
		const std::string &	new_sample,
		bool	drop_haplotypes
	)

help_convert()

void help_convert

(

char **

argv

)

main_convert()

int main_convert	(	int	argc,
		char **	argv
	)

no_multiple_inputs()

void no_multiple_inputs

(

input_type

input

)

Variable Documentation

ALGORITHM_DEFAULT

const algorithm_type ALGORITHM_DEFAULT = algorithm_auto

INPUT_DEFAULT

const input_type INPUT_DEFAULT = input_handlegraph