\documentclass{bioinfo}
\copyrightyear{$copyrightyear$} \pubyear{$pubyear$}


$if(highlighting-macros)$
% Pandoc syntax highlighting
$highlighting-macros$
$endif$

% tightlist command for lists without linebreak
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}

$if(tables)$
% From pandoc table feature
\usepackage{longtable,booktabs,array}
$if(multirow)$
\usepackage{multirow}
$endif$
\usepackage{calc} % for calculating minipage widths
% Correct order of tables after \paragraph or \subparagraph
\usepackage{etoolbox}
\makeatletter
\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
\makeatother
% Allow footnotes in longtable head/foot
\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
\makesavenoteenv{longtable}
$endif$

$if(csl-refs)$
% Pandoc citation processing
$if(pandoc318)$
%From Pandoc 3.1.8
% definitions for citeproc citations
\NewDocumentCommand\citeproctext{}{}
\NewDocumentCommand\citeproc{mm}{%
  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
\makeatletter
 % allow citations to break across lines
 \let\@cite@ofmt\@firstofone
 % avoid brackets around text for \cite:
 \def\@biblabel#1{}
 \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
\makeatother
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newenvironment{CSLReferences}[2] % #1 hanging-indent, #2 entry-spacing
 {\begin{list}{}{%
  \setlength{\itemindent}{0pt}
  \setlength{\leftmargin}{0pt}
  \setlength{\parsep}{0pt}
  % turn on hanging indent if param 1 is 1
  \ifodd #1
   \setlength{\leftmargin}{\cslhangindent}
   \setlength{\itemindent}{-1\cslhangindent}
  \fi
  % set entry spacing
  \setlength{\itemsep}{#2\baselineskip}}}
 {\end{list}}
$else$$if(pandoc317)$
% definitions for citeproc citations
\NewDocumentCommand\citeproctext{}{}
\NewDocumentCommand\citeproc{mm}{%
  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
% avoid brackets around text for \cite:
\makeatletter
 \def\@biblabel#1{}
 \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
\makeatother
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newlength{\cslentryspacing}
\setlength{\cslentryspacing}{0em}
\usepackage{enumitem}
\newlist{CSLReferences}{itemize}{1}
\setlist[CSLReferences]{label={},
  leftmargin=\cslhangindent,
  itemindent=-1\cslhangindent,
  parsep=\parskip,
  itemsep=\cslentryspacing}
$else$
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newlength{\cslentryspacingunit} % times entry-spacing
\setlength{\cslentryspacingunit}{\parskip}
% for Pandoc 2.8 to 2.10.1
\newenvironment{cslreferences}%
  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
  {\par}
% For Pandoc 2.11+
\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
 {% don't indent paragraphs
  \setlength{\parindent}{0pt}
  % turn on hanging indent if param 1 is 1
  \ifodd #1
  \let\oldpar\par
  \def\par{\hangindent=\cslhangindent\oldpar}
  \fi
  % set entry spacing
  \setlength{\parskip}{#2\cslentryspacingunit}
 }%
 {}
$endif$$endif$
\usepackage{calc}
\newcommand{\CSLBlock}[1]{#1\hfill\break}
\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
$endif$

$for(header-includes)$
$header-includes$
$endfor$

% hyperref makes the margins screwy.
% https://groups.google.com/forum/#!topic/latexusersgroup/4W_SwGk6zx4
% http://ansuz.sooke.bc.ca/software/latex-tricks.php
% \usepackage[colorlinks=true, allcolors=blue]{hyperref}

\access{Advance Access Publication Date: $access_date.day$ $access_date.month$ $access_date.year$}
\appnotes{$if(manuscript_type)$$manuscript_type$$else$$subject_section$$endif$}

\begin{document}

$for(include-before)$
$include-before$

$endfor$

\firstpage{1}

\subtitle{$subject_section$}

\title[$title_short$]{$title_full$}

\author[FirstAuthorLastName \textit{et~al}.]{
$for(author)$$author.name$\,\textsuperscript{$author.affiliation$}$sep$, $endfor$
}

\address{
$for(address)$
\textsuperscript{$address.code$}$address.address$\\
$endfor$
}

\corresp{$corresponding_author_text$}

\history{Received on XXX; revised on XXX; accepted on XXX}

\editor{Associate Editor: XXX}

\abstract{
\textbf{Motivation:} $motivation$\\
\textbf{Results:} $results$\\
\textbf{Availability:} $availability$\\
\textbf{Contact:}$corresponding_author_email$\\
\textbf{Supplementary information:} $supplementary_info$}

\maketitle

$body$

$for(include-after)$
$include-after$
$endfor$

% Bibliography
\bibliographystyle{natbib}
\bibliography{$bibliography$}

\end{document}
