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.TH "src/ivar.cpp" 3 "Sun Jul 29 2018" "iVar" \" -*- nroff -*-
.ad l
.nh
.SH NAME
src/ivar.cpp
.SH SYNOPSIS
.br
.PP
\fC#include <iostream>\fP
.br
\fC#include <unistd\&.h>\fP
.br
\fC#include 'remove_reads_from_amplicon\&.h'\fP
.br
\fC#include 'call_consensus_pileup\&.h'\fP
.br
\fC#include 'call_variants\&.h'\fP
.br
\fC#include 'trim_primer_quality\&.h'\fP
.br
\fC#include 'get_masked_amplicons\&.h'\fP
.br
\fC#include 'suffix_tree\&.h'\fP
.br
.SS "Classes"
.in +1c
.ti -1c
.RI "struct \fBargs_t\fP"
.br
.in -1c
.SS "Functions"
.in +1c
.ti -1c
.RI "void \fBprint_usage\fP ()"
.br
.ti -1c
.RI "void \fBprint_trim_usage\fP ()"
.br
.ti -1c
.RI "void \fBprint_variants_usage\fP ()"
.br
.ti -1c
.RI "void \fBprint_filtervariants_usage\fP ()"
.br
.ti -1c
.RI "void \fBprint_consensus_usage\fP ()"
.br
.ti -1c
.RI "void \fBprint_removereads_usage\fP ()"
.br
.ti -1c
.RI "void \fBprint_getmasked_usage\fP ()"
.br
.ti -1c
.RI "void \fBprint_trimadapter_usage\fP ()"
.br
.ti -1c
.RI "void \fBprint_version_info\fP ()"
.br
.ti -1c
.RI "int \fBmain\fP (int argc, char *argv[])"
.br
.in -1c
.SS "Variables"
.in +1c
.ti -1c
.RI "const std::string \fBVERSION\fP = '1\&.0'"
.br
.ti -1c
.RI "struct \fBargs_t\fP \fBg_args\fP"
.br
.in -1c
.SH "Function Documentation"
.PP
.SS "int main (int argc, char * argv[])"
Main Function
.PP
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\&.
.SH "Author"
.PP
Generated automatically by Doxygen for iVar from the source code\&.
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