vg
tools for working with variation graphs
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#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) |
: multipath mapping of reads to a graph
#define OPT_ALWAYS_CHECK_POPULATION 1002 |
#define OPT_APPROX_EXP 1008 |
#define OPT_BAND_PADDING_MULTIPLIER 1012 |
#define OPT_COMPONENT_MIN_DIST 1011 |
#define OPT_FORCE_HAPLOTYPE_COUNT 1004 |
#define OPT_GREEDY_MIN_DIST 1010 |
#define OPT_MAX_PATHS 1009 |
#define OPT_MIN_DIST_CLUSTER 1007 |
#define OPT_PRUNE_EXP 1000 |
#define OPT_RECOMBINATION_PENALTY 1001 |
#define OPT_SUPPRESS_TAIL_ANCHORS 1005 |
#define OPT_TOP_TRACEBACKS 1006 |
void help_mpmap | ( | char ** | argv | ) |
int main_mpmap | ( | int | argc, |
char ** | argv | ||
) |