vg
tools for working with variation graphs
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#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include <cassert>
#include <cstring>
#include <map>
#include <vector>
#include <unordered_set>
#include <chrono>
#include <mutex>
#include "subcommand.hpp"
#include "../seed_clusterer.hpp"
#include "../mapper.hpp"
#include "../annotation.hpp"
#include <vg/io/vpkg.hpp>
#include <vg/io/stream.hpp>
#include "../hts_alignment_emitter.hpp"
#include "../gapless_extender.hpp"
#include "../minimizer_mapper.hpp"
#include "../index_manager.hpp"
#include <bdsg/overlays/overlay_helper.hpp>
#include <gbwtgraph/minimizer.h>
Classes | |
struct | vg::Range< Number > |
This defines a range of values to test, from start to <=end, going up by step. More... | |
struct | vg::is_instantiation_of< Subject, Predicate > |
struct | vg::is_instantiation_of< Predicate< PredicateArgs... >, Predicate > |
Namespaces | |
vg | |
Macros | |
#define | OPT_OUTPUT_BASENAME 1001 |
#define | OPT_REPORT_NAME 1002 |
#define | OPT_TRACK_PROVENANCE 1003 |
#define | OPT_TRACK_CORRECTNESS 1004 |
#define | OPT_FRAGMENT_MEAN 1005 |
#define | OPT_FRAGMENT_STDEV 1006 |
#define | OPT_CLUSTER_STDEV 1007 |
#define | OPT_RESCUE_STDEV 1008 |
Functions | |
template<typename Result > | |
bool | vg::parse (const string &arg, typename enable_if< is_instantiation_of< Result, Range >::value, Result >::type &dest) |
Parse a range as start[:end[:step]]. More... | |
void | help_giraffe (char **argv) |
int | main_giraffe (int argc, char **argv) |
: G(ir)AF (Graph Alignment Format) Fast Emitter: a new mapper that will be extremely fast once we actually write it
#define OPT_CLUSTER_STDEV 1007 |
#define OPT_FRAGMENT_MEAN 1005 |
#define OPT_FRAGMENT_STDEV 1006 |
#define OPT_OUTPUT_BASENAME 1001 |
#define OPT_REPORT_NAME 1002 |
#define OPT_RESCUE_STDEV 1008 |
#define OPT_TRACK_CORRECTNESS 1004 |
#define OPT_TRACK_PROVENANCE 1003 |
void help_giraffe | ( | char ** | argv | ) |
int main_giraffe | ( | int | argc, |
char ** | argv | ||
) |