sim_main.cpp File Reference

#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <list>
#include <fstream>
#include <algorithm>
#include <regex>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../aligner.hpp"
#include "../gbwt_helper.hpp"
#include "vg/io/alignment_emitter.hpp"
#include "../sampler.hpp"
#include <vg/io/protobuf_emitter.hpp>
#include <vg/io/vpkg.hpp>
#include <bdsg/hash_graph.hpp>
#include <bdsg/overlays/overlay_helper.hpp>

Macros
#define	OPT_MULTI_POSITION   1000
#define	OPT_MAX_TRIES   1001

Functions
vector< pair< string, double > >	parse_rsem_expression_file (istream &rsem_in)
vector< tuple< string, string, size_t > >	parse_haplotype_transcript_file (istream &haplo_tx_in)
void	help_sim (char **argv)
int	main_sim (int argc, char **argv)

Detailed Description

Defines the "vg sim" subcommand, which generates potential reads from a graph.

Macro Definition Documentation

OPT_MAX_TRIES

#define OPT_MAX_TRIES   1001

OPT_MULTI_POSITION

#define OPT_MULTI_POSITION   1000

Function Documentation

help_sim()

void help_sim

(

char **

argv

)

main_sim()

int main_sim	(	int	argc,
		char **	argv
	)

parse_haplotype_transcript_file()

vector< tuple< string, string, size_t > > parse_haplotype_transcript_file

(

istream &

haplo_tx_in

)

parse_rsem_expression_file()

vector< pair< string, double > > parse_rsem_expression_file

(

istream &

rsem_in

)