vg
tools for working with variation graphs
Macros | Functions
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_PRUNE_EXP   1000
 
#define OPT_RECOMBINATION_PENALTY   1001
 
#define OPT_ALWAYS_CHECK_POPULATION   1002
 
#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_APPROX_EXP   1008
 
#define OPT_MAX_PATHS   1009
 
#define OPT_GREEDY_MIN_DIST   1010
 
#define OPT_COMPONENT_MIN_DIST   1011
 
#define OPT_BAND_PADDING_MULTIPLIER   1012
 

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_APPROX_EXP

#define OPT_APPROX_EXP   1008

◆ OPT_BAND_PADDING_MULTIPLIER

#define OPT_BAND_PADDING_MULTIPLIER   1012

◆ OPT_COMPONENT_MIN_DIST

#define OPT_COMPONENT_MIN_DIST   1011

◆ OPT_FORCE_HAPLOTYPE_COUNT

#define OPT_FORCE_HAPLOTYPE_COUNT   1004

◆ OPT_GREEDY_MIN_DIST

#define OPT_GREEDY_MIN_DIST   1010

◆ OPT_MAX_PATHS

#define OPT_MAX_PATHS   1009

◆ OPT_MIN_DIST_CLUSTER

#define OPT_MIN_DIST_CLUSTER   1007

◆ OPT_PRUNE_EXP

#define OPT_PRUNE_EXP   1000

◆ OPT_RECOMBINATION_PENALTY

#define OPT_RECOMBINATION_PENALTY   1001

◆ 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 
)