mpmap_main.cpp File Reference

#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include "subcommand.hpp"
#include <vg/io/vpkg.hpp>
#include "../multipath_mapper.hpp"
#include "../path.hpp"
#include "../xg.hpp"
#include "../watchdog.hpp"
#include <bdsg/overlay_helper.hpp>

Macros
#define	OPT_SCORE_MATRIX   1000
#define	OPT_RECOMBINATION_PENALTY   1001
#define	OPT_ALWAYS_CHECK_POPULATION   1002
#define	OPT_DELAY_POPULATION_SCORING   1003
#define	OPT_FORCE_HAPLOTYPE_COUNT   1004
#define	OPT_SUPPRESS_TAIL_ANCHORS   1005
#define	OPT_TOP_TRACEBACKS   1006
#define	OPT_MIN_DIST_CLUSTER   1007
#define	OPT_REPORT_GROUP_MAPQ   1008

Functions
void	help_mpmap (char **argv)
int	main_mpmap (int argc, char **argv)

Detailed Description

: multipath mapping of reads to a graph

Macro Definition Documentation

OPT_ALWAYS_CHECK_POPULATION

#define OPT_ALWAYS_CHECK_POPULATION   1002

OPT_DELAY_POPULATION_SCORING

#define OPT_DELAY_POPULATION_SCORING   1003

OPT_FORCE_HAPLOTYPE_COUNT

#define OPT_FORCE_HAPLOTYPE_COUNT   1004

OPT_MIN_DIST_CLUSTER

#define OPT_MIN_DIST_CLUSTER   1007

OPT_RECOMBINATION_PENALTY

#define OPT_RECOMBINATION_PENALTY   1001

OPT_REPORT_GROUP_MAPQ

#define OPT_REPORT_GROUP_MAPQ   1008

OPT_SCORE_MATRIX

#define OPT_SCORE_MATRIX   1000

OPT_SUPPRESS_TAIL_ANCHORS

#define OPT_SUPPRESS_TAIL_ANCHORS   1005

OPT_TOP_TRACEBACKS

#define OPT_TOP_TRACEBACKS   1006

Function Documentation

help_mpmap()

void help_mpmap

(

char **

argv

)

main_mpmap()

int main_mpmap	(	int	argc,
		char **	argv
	)