#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>

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

#define	OPT_HARD_HIT_MAX_MULTIPLIER 1013

#define	OPT_MAX_RESCUE_ATTEMPTS 1014

#define	OPT_STRIP_LENGTH 1015

#define	OPT_STRIP_COUNT 1016

#define	OPT_SECONDARY_RESCUE_ATTEMPTS 1017

#define	OPT_SECONDARY_MAX_DIFF 1018

#define	OPT_NO_CLUSTER 1019

#define	OPT_NO_GREEDY_MEM_RESTARTS 1020

#define	OPT_GREEDY_MEM_RESTART_MAX_LCP 1021

#define	OPT_SHORT_MEM_FILTER_FACTOR 1022

#define	OPT_NO_OUTPUT 1023

#define	OPT_STRIPPED_MATCH 1024

#define	OPT_FAN_OUT_QUAL 1025

#define	OPT_MAX_FANS_OUT 1026

#define	OPT_FAN_OUT_DIFF 1027

#define	OPT_PATH_RESCUE_GRAPH 1028

#define	OPT_MAX_RESCUE_P_VALUE 1029

#define	OPT_ALT_PATHS 1030

#define	OPT_SUPPRESS_SUPPRESSION 1031

#define	OPT_SNARL_MAX_CUT 1032

#define	OPT_SPLICE_ODDS 1033

#define	OPT_REPORT_ALLELIC_MAPQ 1034

#define	OPT_RESEED_LENGTH 1035

#define	OPT_MAX_MOTIF_PAIRS 1036

#define	OPT_SUPPRESS_MISMAPPING_DETECTION 1037

#define	OPT_DROP_SUBGRAPH 1038

#define	OPT_REF_NAME 1039

Functions
pair< vector< double >, vector< pair< double, double > > >	parse_intron_distr_file (ifstream &strm)

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_ALT_PATHS

#define OPT_ALT_PATHS 1030

◆ 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_DROP_SUBGRAPH

#define OPT_DROP_SUBGRAPH 1038

◆ OPT_FAN_OUT_DIFF

#define OPT_FAN_OUT_DIFF 1027

◆ OPT_FAN_OUT_QUAL

#define OPT_FAN_OUT_QUAL 1025

◆ OPT_FORCE_HAPLOTYPE_COUNT

#define OPT_FORCE_HAPLOTYPE_COUNT 1004

◆ OPT_GREEDY_MEM_RESTART_MAX_LCP

#define OPT_GREEDY_MEM_RESTART_MAX_LCP 1021

◆ OPT_GREEDY_MIN_DIST

#define OPT_GREEDY_MIN_DIST 1010

◆ OPT_HARD_HIT_MAX_MULTIPLIER

#define OPT_HARD_HIT_MAX_MULTIPLIER 1013

◆ OPT_MAX_FANS_OUT

#define OPT_MAX_FANS_OUT 1026

◆ OPT_MAX_MOTIF_PAIRS

#define OPT_MAX_MOTIF_PAIRS 1036

◆ OPT_MAX_PATHS

#define OPT_MAX_PATHS 1009

◆ OPT_MAX_RESCUE_ATTEMPTS

#define OPT_MAX_RESCUE_ATTEMPTS 1014

◆ OPT_MAX_RESCUE_P_VALUE

#define OPT_MAX_RESCUE_P_VALUE 1029

◆ OPT_MIN_DIST_CLUSTER

#define OPT_MIN_DIST_CLUSTER 1007

◆ OPT_NO_CLUSTER

#define OPT_NO_CLUSTER 1019

◆ OPT_NO_GREEDY_MEM_RESTARTS

#define OPT_NO_GREEDY_MEM_RESTARTS 1020

◆ OPT_NO_OUTPUT

#define OPT_NO_OUTPUT 1023

◆ OPT_PATH_RESCUE_GRAPH

#define OPT_PATH_RESCUE_GRAPH 1028

◆ OPT_PRUNE_EXP

#define OPT_PRUNE_EXP 1000

◆ OPT_RECOMBINATION_PENALTY

#define OPT_RECOMBINATION_PENALTY 1001

◆ OPT_REF_NAME

#define OPT_REF_NAME 1039

◆ OPT_REPORT_ALLELIC_MAPQ

#define OPT_REPORT_ALLELIC_MAPQ 1034

◆ OPT_RESEED_LENGTH

#define OPT_RESEED_LENGTH 1035

◆ OPT_SECONDARY_MAX_DIFF

#define OPT_SECONDARY_MAX_DIFF 1018

◆ OPT_SECONDARY_RESCUE_ATTEMPTS

#define OPT_SECONDARY_RESCUE_ATTEMPTS 1017

◆ OPT_SHORT_MEM_FILTER_FACTOR

#define OPT_SHORT_MEM_FILTER_FACTOR 1022

◆ OPT_SNARL_MAX_CUT

#define OPT_SNARL_MAX_CUT 1032

◆ OPT_SPLICE_ODDS

#define OPT_SPLICE_ODDS 1033

◆ OPT_STRIP_COUNT

#define OPT_STRIP_COUNT 1016

◆ OPT_STRIP_LENGTH

#define OPT_STRIP_LENGTH 1015

◆ OPT_STRIPPED_MATCH

#define OPT_STRIPPED_MATCH 1024

◆ OPT_SUPPRESS_MISMAPPING_DETECTION

#define OPT_SUPPRESS_MISMAPPING_DETECTION 1037

◆ OPT_SUPPRESS_SUPPRESSION

#define OPT_SUPPRESS_SUPPRESSION 1031

◆ 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
	)

◆ parse_intron_distr_file()

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

Macros

Functions