\hypertarget{ivar_8cpp}{}\section{src/ivar.cpp File Reference}
\label{ivar_8cpp}\index{src/ivar.\+cpp@{src/ivar.\+cpp}}
{\ttfamily \#include $<$iostream$>$}\newline
{\ttfamily \#include $<$unistd.\+h$>$}\newline
{\ttfamily \#include \char`\"{}remove\+\_\+reads\+\_\+from\+\_\+amplicon.\+h\char`\"{}}\newline
{\ttfamily \#include \char`\"{}call\+\_\+consensus\+\_\+pileup.\+h\char`\"{}}\newline
{\ttfamily \#include \char`\"{}call\+\_\+variants.\+h\char`\"{}}\newline
{\ttfamily \#include \char`\"{}trim\+\_\+primer\+\_\+quality.\+h\char`\"{}}\newline
{\ttfamily \#include \char`\"{}get\+\_\+masked\+\_\+amplicons.\+h\char`\"{}}\newline
{\ttfamily \#include \char`\"{}suffix\+\_\+tree.\+h\char`\"{}}\newline
\subsection*{Classes}
\begin{DoxyCompactItemize}
\item 
struct \mbox{\hyperlink{structargs__t}{args\+\_\+t}}
\end{DoxyCompactItemize}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
\mbox{\Hypertarget{ivar_8cpp_ae5ad5cbeccaedc03a48d3c7eaa803e79}\label{ivar_8cpp_ae5ad5cbeccaedc03a48d3c7eaa803e79}} 
void {\bfseries print\+\_\+usage} ()
\item 
\mbox{\Hypertarget{ivar_8cpp_a7d3d88c60168244994ebfb9d01d71aad}\label{ivar_8cpp_a7d3d88c60168244994ebfb9d01d71aad}} 
void {\bfseries print\+\_\+trim\+\_\+usage} ()
\item 
\mbox{\Hypertarget{ivar_8cpp_a26b660ffee9302a25fc4b85b6fa7f9d9}\label{ivar_8cpp_a26b660ffee9302a25fc4b85b6fa7f9d9}} 
void {\bfseries print\+\_\+variants\+\_\+usage} ()
\item 
\mbox{\Hypertarget{ivar_8cpp_a494f2b3c1101c4424b73e80d33e4be09}\label{ivar_8cpp_a494f2b3c1101c4424b73e80d33e4be09}} 
void {\bfseries print\+\_\+filtervariants\+\_\+usage} ()
\item 
\mbox{\Hypertarget{ivar_8cpp_a8499b57df7ba0c00092dd1fd724cd445}\label{ivar_8cpp_a8499b57df7ba0c00092dd1fd724cd445}} 
void {\bfseries print\+\_\+consensus\+\_\+usage} ()
\item 
\mbox{\Hypertarget{ivar_8cpp_afab6040035caaef89097988ea732ed2c}\label{ivar_8cpp_afab6040035caaef89097988ea732ed2c}} 
void {\bfseries print\+\_\+removereads\+\_\+usage} ()
\item 
\mbox{\Hypertarget{ivar_8cpp_a27fcc15b0b3c8b4386694af97f09fb91}\label{ivar_8cpp_a27fcc15b0b3c8b4386694af97f09fb91}} 
void {\bfseries print\+\_\+getmasked\+\_\+usage} ()
\item 
\mbox{\Hypertarget{ivar_8cpp_ac27b7b01a0eb74231c25b3afe477dcae}\label{ivar_8cpp_ac27b7b01a0eb74231c25b3afe477dcae}} 
void {\bfseries print\+\_\+trimadapter\+\_\+usage} ()
\item 
\mbox{\Hypertarget{ivar_8cpp_a576fe250f6f9abb50069a9022632052f}\label{ivar_8cpp_a576fe250f6f9abb50069a9022632052f}} 
void {\bfseries print\+\_\+version\+\_\+info} ()
\item 
int \mbox{\hyperlink{ivar_8cpp_a0ddf1224851353fc92bfbff6f499fa97}{main}} (int argc, char $\ast$argv\mbox{[}$\,$\mbox{]})
\end{DoxyCompactItemize}
\subsection*{Variables}
\begin{DoxyCompactItemize}
\item 
\mbox{\Hypertarget{ivar_8cpp_a1e20c163c03189acfe600030f8ef8b95}\label{ivar_8cpp_a1e20c163c03189acfe600030f8ef8b95}} 
const std\+::string {\bfseries V\+E\+R\+S\+I\+ON} = \char`\"{}1.\+0\char`\"{}
\item 
\mbox{\Hypertarget{ivar_8cpp_aefc57f4c7b665d04123350d1d1b9fbff}\label{ivar_8cpp_aefc57f4c7b665d04123350d1d1b9fbff}} 
struct \mbox{\hyperlink{structargs__t}{args\+\_\+t}} {\bfseries g\+\_\+args}
\end{DoxyCompactItemize}


\subsection{Function Documentation}
\mbox{\Hypertarget{ivar_8cpp_a0ddf1224851353fc92bfbff6f499fa97}\label{ivar_8cpp_a0ddf1224851353fc92bfbff6f499fa97}} 
\index{ivar.\+cpp@{ivar.\+cpp}!main@{main}}
\index{main@{main}!ivar.\+cpp@{ivar.\+cpp}}
\subsubsection{\texorpdfstring{main()}{main()}}
{\footnotesize\ttfamily int main (\begin{DoxyParamCaption}\item[{int}]{argc,  }\item[{char $\ast$}]{argv\mbox{[}$\,$\mbox{]} }\end{DoxyParamCaption})}

Main Function

This is where the command line arguments into i\+Var are parsed. i\+Var first parses the first argument and depending on the command it either returns the version or uses G\+NU getopt to parse the remaining arguments. 