mpmap_main.cpp File Reference

#include <omp.h>
#include <unistd.h>
#include <ctime>
#include <getopt.h>
#include <thread>
#include <atomic>
#include <mutex>
#include <list>
#include "subcommand.hpp"
#include <vg/io/vpkg.hpp>
#include "../algorithms/component.hpp"
#include "../algorithms/pad_band.hpp"
#include "../multipath_mapper.hpp"
#include "../mem_accelerator.hpp"
#include "../surjector.hpp"
#include "../multipath_alignment_emitter.hpp"
#include "../path.hpp"
#include "../watchdog.hpp"
#include <bdsg/overlays/overlay_helper.hpp>
#include <bdsg/packed_graph.hpp>
#include <bdsg/hash_graph.hpp>
#include <xg.hpp>

Functions
pair< vector< double >, vector< pair< double, double > > >	parse_intron_distr_file (const Logger &logger, ifstream &strm)
void	help_mpmap (char **argv)
int	main_mpmap (int argc, char **argv)

Detailed Description

: multipath mapping of reads to a graph

Function Documentation

help_mpmap()

void help_mpmap

(

char **

argv

)

main_mpmap()

int main_mpmap	(	int	argc,
		char **	argv
	)

parse_intron_distr_file()

pair<vector<double>, vector<pair<double, double> > > parse_intron_distr_file	(	const Logger &	logger,
		ifstream &	strm
	)