thesis.tex

\documentclass[10pt]{book}
\usepackage[a5paper]{geometry}
\usepackage{mathpazo} % font style
\linespread{1.05} % Palatino needs more leading (space between lines)
\renewcommand{\familydefault}{\sfdefault}
\input{usepackages.tex} % load required packages
\raggedbottom % prevent spreading out paragraphs with lots of whitespace inbetween

\begin{document}

\pagestyle{empty}

\input{cover.tex}

\setcounter{page}{1}

\input{preamble.tex}

\tableofcontents

\pagestyle{fancy}
\fancyhf{}
\fancyhead[LE]{\leftmark}
\fancyhead[RO]{\rightmark}
\fancyfoot[LE,RO]{\thepage}

\input{introduction.tex}
\input{xgap.tex}
\input{xqtl.tex}
\input{wormqtl.tex}
\input{caddmmr.tex}
\input{gavin.tex}
\input{frameworkforgenomics.tex}
\input{discussion.tex}

\bibliographystyle{plain}

\cleardoublepage
\leftwatermark{}\rightwatermark{} % stop printing the thumb indexes
\phantomsection\bibliography{references}{}
\cleardoublepage\phantomsection\listoftables
\cleardoublepage\phantomsection\listoffigures

\input{appendix.tex}

\input{back.tex}

\end{document}