ivar.cpp File Reference

#include <iostream>
#include <unistd.h>
#include "remove_reads_from_amplicon.h"
#include "call_consensus_pileup.h"
#include "call_variants.h"
#include "trim_primer_quality.h"
#include "get_masked_amplicons.h"
#include "suffix_tree.h"

Classes
struct	args_t

Functions
void	print_usage ()
void	print_trim_usage ()
void	print_variants_usage ()
void	print_filtervariants_usage ()
void	print_consensus_usage ()
void	print_removereads_usage ()
void	print_getmasked_usage ()
void	print_trimadapter_usage ()
void	print_version_info ()
int	main (int argc, char *argv[])

Variables
const std::string	VERSION = "1.0"
struct args_t	g_args

Function Documentation

main()

int main	(	int	argc,
		char *	argv[]
	)

Main Function

This is where the command line arguments into iVar are parsed. iVar first parses the first argument and depending on the command it either returns the version or uses GNU getopt to parse the remaining arguments.