\section{File List}
Here is a list of all documented files with brief descriptions\+:\begin{DoxyCompactList}
\item\contentsline{section}{src/{\bfseries alignment.\+h} }{\pageref{alignment_8h}}{}
\item\contentsline{section}{src/{\bfseries allele\+\_\+functions.\+h} }{\pageref{allele__functions_8h}}{}
\item\contentsline{section}{src/{\bfseries call\+\_\+consensus\+\_\+pileup.\+h} }{\pageref{call__consensus__pileup_8h}}{}
\item\contentsline{section}{src/{\bfseries call\+\_\+variants.\+h} }{\pageref{call__variants_8h}}{}
\item\contentsline{section}{src/{\bfseries get\+\_\+masked\+\_\+amplicons.\+h} }{\pageref{get__masked__amplicons_8h}}{}
\item\contentsline{section}{src/\mbox{\hyperlink{ivar_8cpp}{ivar.\+cpp}} }{\pageref{ivar_8cpp}}{}
\item\contentsline{section}{src/{\bfseries primer\+\_\+bed.\+h} }{\pageref{primer__bed_8h}}{}
\item\contentsline{section}{src/{\bfseries remove\+\_\+reads\+\_\+from\+\_\+amplicon.\+h} }{\pageref{remove__reads__from__amplicon_8h}}{}
\item\contentsline{section}{src/{\bfseries suffix\+\_\+tree.\+h} }{\pageref{suffix__tree_8h}}{}
\item\contentsline{section}{src/{\bfseries trim\+\_\+primer\+\_\+quality.\+h} }{\pageref{trim__primer__quality_8h}}{}
\end{DoxyCompactList}