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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 acronym is for {\em Species Perscrutandis Enixe Locis Locabutur}. This means {\em The characters will be localized using an zealous loci inspection}, the very purpose of the software. If you read this manual, you already know what QTL stands for. 

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. 

\paragraph{} When the project started, we were just planning to rewrite our legacy code MCQTL, using modern C++. After decades of development and many contributors - most of them not even reachable  - MCQTL had reached the stage of "Hydra code": every bug correction, every improvement was made at very high cost.

 As the project was moving forward, and as we were thinking it would be a quick and easy release, we discover that some hypothesis that were made in MCQTL, were no mode valid with dealing with modern crosses (MAGIC, AIC...)

This work switched from engineering project to research project  inadvertently, and we are very happy about that ! 
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\paragraph{} Both the software and this manual are work under progress: feed-back is welcome and appreciated. 
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\vspace*{\fill}
\noindent Spell-QTL is available at \url{https://mulcyber.toulouse.inra.fr/frs/?group_id=204} under Gnu Public License. 
\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}