thesis.tex

\documentclass[UKenglish]{ifimaster}
\usepackage[utf8]{inputenc}           
\usepackage[T1]{fontenc,url}
\usepackage{mdframed}
\usepackage{caption}
\usepackage{tikz}
\usepackage{pgfplots}
\usepackage{amsthm}
\usepackage{amsmath}
\usepackage{color,soul}
\usepackage{wrapfig}
\usepackage{subcaption}
\usepackage{dsfont}
\usepackage{listings}
\usepackage{floatrow,subfig}
\usepackage{tabularx}
\usepackage{listings}
\usepackage{thmtools}
\usepackage[toc,page]{appendix}
\usepackage{float}
\usepackage{mathtools}
\usepackage{csquotes}
\usepackage[]{algorithm2e}
\usepackage[nomessages]{fp}
\usepackage{babel,textcomp,csquotes,ifimasterforside,varioref,graphicx}
\usepackage[backend=biber,style=numeric-comp]{biblatex}
\usetikzlibrary{automata,arrows,positioning,matrix}
\usepgfplotslibrary{fillbetween}
\usepackage{ifthen}
\usepackage[noend]{algpseudocode}

\newcommand{\hlcyan}[1]{{\sethlcolor{cyan}\hl{#1}}}

\newcommand{\HeatmapNode}[1]{
  \ifthenelse{#1 < 50}
  {
    \FPeval\col{100-2*#1}
    \node [fill=red!\col] {#1};
  }
  % else
  {
    \FPeval\col{100-2*(100-#1)}
    \node [fill=green!\col] {#1};
  }
}

% Fix footnotes breaking pages
\interfootnotelinepenalty=10000

% Fix footnote indentation
\usepackage[hang,flushmargin]{footmisc}


\newtheoremstyle{break}
  {\topsep}{\topsep}%
  {\itshape}{}%
  {\bfseries}{}%
  {\newline}{}%
\theoremstyle{break}
\newtheorem{defn}{Definition}
\newtheorem{corollary}{Corollary}
\newtheorem{assumption}{Assumption}

\renewcommand{\footnoterule}{%
  \kern -3pt
  \hrule width \textwidth height 1pt
  \kern 2pt
}

\usepackage{subfiles}
 
\usepackage{blindtext}

\title{Aligning reads against a graph based reference genome}        
\subtitle{Approximate searches in large and complex structures}        
\author{Esten H{\o}yland Leonardsen}                       

\bibliography{thesis}                  

\begin{document}
\ififorside{}
\frontmatter{}
\maketitle{}

\subfile{abstract}
\subfile{acknowledgements}               

\tableofcontents{}
\listoffigures{}
\listoftables{}
\listoftheorems[ignoreall,show={defn}]

\mainmatter{}
\subfile{introduction}
\subfile{background}
\subfile{methodology}
\subfile{algorithm}
\subfile{validation}
\subfile{performance}
\subfile{discussion}
\subfile{further_work}
\nocite{*}
\printbibliography
\begin{appendices}
\subfile{proof}
\subfile{analysis}
\subfile{tool}
\subfile{birthday_problem}
\end{appendices}
\backmatter{}
\end{document}