depth_main.cpp File Reference

#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <algorithm>
#include <iostream>
#include "subcommand.hpp"
#include <vg/io/vpkg.hpp>
#include <vg/io/stream.hpp>
#include "../handle.hpp"
#include <bdsg/overlays/overlay_helper.hpp>
#include "../utility.hpp"
#include "../packer.hpp"
#include "algorithms/coverage_depth.hpp"

Functions
void	help_depth (char **argv)
int	main_depth (int argc, char **argv)

Variables
const size_t	DEFAULT_MAX_NODES = 1000000
const size_t	DEFAULT_MIN_MAPQ = 0
const size_t	DEFAULT_BIN_SIZE = 1
const size_t	DEFAULT_MIN_COVERAGE = 1

Detailed Description

Estimate sequencing depth from a (packed) alignment.

Function Documentation

help_depth()

void help_depth

(

char **

argv

)

main_depth()

int main_depth	(	int	argc,
		char **	argv
	)

Variable Documentation

DEFAULT_BIN_SIZE

const size_t DEFAULT_BIN_SIZE = 1

DEFAULT_MAX_NODES

const size_t DEFAULT_MAX_NODES = 1000000

DEFAULT_MIN_COVERAGE

const size_t DEFAULT_MIN_COVERAGE = 1

DEFAULT_MIN_MAPQ

const size_t DEFAULT_MIN_MAPQ = 0