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\documentclass[oneside,10pt,DIV=11]{scrreprt}
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\usepackage[toc,page]{appendix}
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\usepackage{varioref}
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\usepackage{url}
\usepackage{listings}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{mathtools}
\usepackage{braket}
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\usepackage{hyperref} %required by pandoc
\usepackage{svg}
\usepackage{import} %required for svg inkscape import
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\usepackage{forest}
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\usepackage{inconsolata} % alternative typewriter font
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\usepackage{hyperref}
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\usepackage[T1]{fontenc} %ensures copy paste work with underscores !
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\graphicspath{{images/}}

\renewcommand{\lstlistingname}{Sample file}
\renewcommand{\lstlistlistingname}{List of \lstlistingname s}
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\lstset{
breakatwhitespace=false,
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breaklines=false,
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basicstyle=\ttfamily
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}

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% required by pandoc... should be in a pandoc.sty file
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\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}


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% 
% \newcommand\myfolder[2][white]{%
% \begin{tikzpicture}[overlay]
% \begin{scope}[xshift=20pt]
% \filldraw[rounded corners=1pt,fill=#1,draw=white,double=black]
%   (-23pt,10pt) -- ++(3pt,5pt) -- ++(18pt,0pt) -- ++(40:3pt) -- ++(9pt,0pt) -- ++(-40:3pt)
%   -- (20pt,15pt) -- (23pt,10pt) -- cycle;
% \filldraw[rounded corners,draw=white,double=black,top color=#1,bottom color=#1!30]
%   (-22pt,-12pt) -- ++(44pt,0pt) -- (25pt,12pt) coordinate (topr) -- ++(-50pt,0pt) coordinate (topl) -- cycle;
% \end{scope}  
% \end{tikzpicture}%
% \makebox[35pt]{\raisebox{-3pt}{{\ttfamily/#2}}}%
% }
% 
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\subject{\includegraphics[width=0.25\textwidth]{images/logotype-INRA-RVB.jpg}}
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\title{Spell-QTL User Manual}
\subtitle{Species perscrutandis enixe locis locabuntur}
\author{Damien Leroux \and Sylvain Jasson}
\date{Version 
\input{version.tex}
}
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\publishers{\includegraphics[width=0.35\textwidth]{images/logo_MIAT.png}
}
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%\lowertitleback{This manual is licensed under a \href{https://creativecommons.org/licenses/by-sa/4.0/}{Creative Commons Attribution-ShareAlike 4.0 International License}.
%\begin{center}
%\includegraphics{images/by-sa.pdf}
%\end{center}}

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\begin{document}
\maketitle


\chapter*{Foreword}

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\paragraph{} Spell-QTL is a software suite allowing to detect QTLs in any crossing design. Spell is an acronym that stands for {\em Species Perscrutandis Enixe Locis Locabutur}. This means {\em The characters will be localized by zealously inspecting the loci}, the very purpose of the software. If you are reading this manual, you already know what QTL stands for. 
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We---Damien Leroux and Sylvain Jasson---are developping Spell-QTL at MIAT, a research lab from INRA French National Institute for Agricultural Research. We are located near Toulouse, in the French Occitanie region. 
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\paragraph{} When the project started, we were just planning to rewrite our legacy code MCQTL, using modern C++. After decades of development and many temporary contributors---most of them not even reachable---MCQTL was in a stage of ``Hydra code'': every bug correction, every improvement had a very high cost.
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As the project was moving forward, and as we were thinking it would be a quick and easy release, we discovered that some hypotheses that were made in MCQTL, were no more valid when dealing with modern crosses (MAGIC, AIC...)
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This work switched inadvertently from an engineering project to a research project, and we are very happy about that! 
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\paragraph{} Both the software and this manual are works in progress: feedback is welcome and appreciated. 
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\vspace*{\fill}
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\noindent Spell-QTL is available at \url{https://mulcyber.toulouse.inra.fr/frs/?group_id=204} under the Gnu Public License. 
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\begin{center}
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\includegraphics[clip, trim=0.5cm 7.9cm 0.5cm 14cm,width=0.25\columnwidth]{pdfs/gpl-v3-logo}
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\end{center}
This manual is licensed under a \href{https://creativecommons.org/licenses/by-sa/4.0/}{Creative Commons Attribution-ShareAlike 4.0 International License}.
\begin{center}
\includegraphics[width=0.25\columnwidth]{pdfs/by-sa}
\end{center}
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\input{pipeline.tex}
\input{outputs.tex}
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\input{detection.tex}
\input{pop.tex}
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\begin{appendices}

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\chapter{\texttt{spell-pedigree} man page} \label{ch:spell:predigree}
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\sloppy
\input{spell-pedigree.tex}
\fussy
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\chapter{\texttt{spell-marker} man page} \label{ch:spell:marker}
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\sloppy
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\input{spell-marker.tex}
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\fussy
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\chapter{\texttt{spell-qtl} man page}
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\sloppy
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\input{spell-qtl.tex}
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\fussy
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\chapter{spell-qtl-examples man page}
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\sloppy
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\input{spell-qtl-examples.tex}
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\fussy
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\end{appendices}
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\lstlistoflistings
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\tableofcontents
\end{document}