main.tex

	%%
%% Modified by Ricardo Garcia-Rosas to satisfy the rules established by the University of Melbourne's Research Higher Degrees Committee as of 4th of June 2019.
%% Guidelines can be found at: https://gradresearch.unimelb.edu.au/__data/assets/pdf_file/0004/2027839/Preparation-of-GR-theses-rules.pdf
%%
%%
%% ----------------------------------------------------------------
%% Thesis.tex -- MAIN FILE (the one that you compile with LaTeX)
%% ---------------------------------------------------------------- 

% Set up the document
\documentclass[a4paper, 11pt, oneside]{Thesis}  % Use the "Thesis" style, based on the ECS Thesis style by Steve Gunn
%
% Put your figures in this directory
\graphicspath{Figures/}  % Location of the graphics files (set up for graphics to be in PDF format)
%


% Include any extra LaTeX packages required
\usepackage[british]{babel}
\usepackage[ddmmyyyy]{datetime}
% with babel and biblatex, csquuotes is a requirements for quoted text to work as expected
\usepackage{csquotes}

%better fonts
\usepackage{lmodern}
%\usepackage[proportional,scaled=1.064]{erewhon}
%\usepackage{heuristica}
%\usepackage[heuristica,vvarbb,bigdelims]{newtxmath}


%\usepackage[light]{CrimsonPro}
\usepackage[T1]{fontenc}
%% The font package uses mweights.sty which has some issues with the
%% \normalfont command. The following two lines fixes this issue.
%\let\oldnormalfont\normalfont
%\def\normalfont{\oldnormalfont\mdseries}


\usepackage[usenames,dvipsnames,table]{xcolor}
%allow clines with background colours
\usepackage{hhline}

%make numbers nicer
\usepackage{siunitx}

%allows bold math symbol
\usepackage{amsmath}
\newcommand\Alpha{\mathrm{A}}
\newcommand\Beta{\mathrm{B}}

%reference managing
\usepackage[sorting=none, citestyle=numeric-comp, sortcites, backend=biber, giveninits=true]{biblatex}
\addbibresource{MyBibLatex.bib}

% we allow the urls in the bibliography to be broken after normal characters as well, not just '-', '\' and '.'
% If you want to break on URL numbers
\setcounter{biburlnumpenalty}{9000}
% If you want to break on URL lower case letters
\setcounter{biburllcpenalty}{9000}
% If you want to break on URL UPPER CASE letters
\setcounter{biburlucpenalty}{9000}

\usepackage{verbatim}  % Needed for the "comment" environment to make LaTeX comments


%setup the links the right way
\hypersetup{urlcolor=blue, colorlinks=true}  % Colours hyperlinks in blue, but this can be distracting if there are many links.

%autoref shouldnt say subsection and subsubsection and section should be upper case
\renewcommand{\sectionautorefname}{Section}
\let\subsectionautorefname\sectionautorefname
\let\subsubsectionautorefname\sectionautorefname
\let\paragraphautorefname\sectionautorefname

\renewcommand{\chapterautorefname}{Chapter}

%make it so that paragraphs are also numbered
\setcounter{secnumdepth}{5}
%and have a newline after them
\usepackage{titlesec}
\titleformat{\paragraph}[hang]{\normalfont\normalsize\bfseries}{\theparagraph}{1em}{}
\titlespacing*{\paragraph}{0pt}{3.25ex plus 1ex minus .2ex}{0.5em}

%make the font normal
\urlstyle{rm}

%allow short citations in the beginning of chapters
\usepackage{epigraph}
% and set it up
\renewcommand{\epigraphsize}{\small\itshape}
\setlength\epigraphwidth{9.5cm}


%this redefines how chapters look and also allows quotes
\usepackage[avantgarde]{quotchap}
%make the title left justified
\makeatletter
\patchcmd{\@makechapterhead}
 {\raggedleft\advance}
 {\raggedright\advance}
 {}{}
\makeatother
%reduce the spacing after a chapter
\renewcommand{\chapterheadendvskip}{\vspace*{0.7\baselineskip}}



% allow marks and todos !!! REMOVE FOR FINAL VERSION !!!
\setlength{\marginparwidth}{2cm}

\usepackage[colorinlistoftodos, prependcaption,textsize=small]{todonotes}


%allows us to use figures nicer
\usepackage{float}

%allows a nice way to "flush" floats
\usepackage{afterpage}


%allows multi column for the paper 
\usepackage{multicol}
\usepackage{tabularray}

%inline lists
\usepackage[inline]{enumitem}

%tables with multirows
\usepackage{array}
\newcommand{\PreserveBackslash}[1]{\let\temp=\\#1\let\\=\temp}
\newcolumntype{C}[1]{>{\PreserveBackslash\centering}p{#1}}
\newcolumntype{R}[1]{>{\PreserveBackslash\raggedleft}p{#1}}
\newcolumntype{L}[1]{>{\PreserveBackslash\raggedright}p{#1}}

\usepackage{multirow}


%%% just in case we want a list of equations in the front
\usepackage[subfigure,titles]{tocloft}
\newcommand{\listequationsname}{List of Equations}
\newlistof{myequations}{equ}{\listequationsname}
\newcommand{\myequation}[2][AAA]{%
	\addcontentsline{equ}{myequations}{\protect\numberline{#1}{\ignorespaces #2}}\par
}
\setlength{\cftmyequationsnumwidth}{3em}    % Length must be defined before it can be set - it isn't defined until you've created the new list
\setlength{\cftmyequationsindent}{\cfttabindent}


\definecolor{codegreen}{rgb}{0,0.6,0}
\definecolor{codegray}{rgb}{0.5,0.5,0.5}
\definecolor{codepurple}{rgb}{0.58,0,0.82}
\definecolor{backcolour}{rgb}{0.98,0.98,0.93}

\lstdefinestyle{mystyle}{
    backgroundcolor=\color{backcolour},   
    commentstyle=\color{codegreen},
    keywordstyle=\color{magenta},
    numberstyle=\tiny\color{codegray},
    stringstyle=\color{codepurple},
    basicstyle=\ttfamily\footnotesize,
    breakatwhitespace=false,         
    breaklines=true,                 
    captionpos=t,                    
    keepspaces=true,                 
    numbers=left,                    
    numbersep=5pt,                  
    showspaces=false,                
    showstringspaces=false,
    showtabs=false,                  
    tabsize=2
}

\lstset{style=mystyle}



%adjust the appendix page command, because its really boring and ugly by itself
\renewcommand\appendixpage{
  %\btypeout{\appendixpagename}
  \thispagestyle{empty}
  \null\vfil
  \begin{center}
    \setlength{\parskip}{0pt}
    \bigskip
    {\huge{\textit{\appendixpagename}} \par}
    \medskip
    {\normalsize by \authornames \par}
    \bigskip
    {contains:
    \begin{itemize}[leftmargin=5.5cm]
    	\item published manuscripts
    	\item supplementary method
    	\item supplementary figures
    \end{itemize}
    }
  \end{center}
  \vfil\vfil\vfil\null
  \cleardoublepage
}

%% ----------------------------------------------------------------

%allow multi autoref
\makeatletter

% define a macro \Autoref to allow multiple references to be passed to \autoref
\newcommand\Autoref[1]{\@first@ref#1,@}
\def\@throw@dot#1.#2@{#1}% discard everything after the dot
\def\@set@refname#1{%    % set \@refname to autoefname+s using \getrefbykeydefault
    \edef\@tmp{\getrefbykeydefault{#1}{anchor}{}}%
    \xdef\@tmp{\expandafter\@throw@dot\@tmp.@}%
    \ltx@IfUndefined{\@tmp autorefnameplural}%
         {\def\@refname{\@nameuse{\@tmp autorefname}s}}%
         {\def\@refname{\@nameuse{\@tmp autorefnameplural}}}%
}
\def\@first@ref#1,#2{%
  \ifx#2@\autoref{#1}\let\@nextref\@gobble% only one ref, revert to normal \autoref
  \else%
    \@set@refname{#1}%  set \@refname to autoref name
    \@refname~\ref{#1}% add autoefname and first reference
    \let\@nextref\@next@ref% push processing to \@next@ref
  \fi%
  \@nextref#2%
}
\def\@next@ref#1,#2{%
   \ifx#2@, and~\ref{#1}\let\@nextref\@gobble% at end: print and+\ref and stop
   \else, \ref{#1}% print  ,+\ref and continue
   \fi%
   \@nextref#2%
}

\makeatother




%% ----------------------------------------------------------------

% custom hyphenation
\hyphenation{germ-line}
\hyphenation{me-la-no-ma}
\hyphenation{anti-tu-mour-i-gen-ic}
\hyphenation{nu-cle-o-tide}


\Urlmuskip = 0mu plus 1mu


% hide anything lower than section in the TOC
\setcounter{tocdepth}{2}

%exchange finalnew for margins for the final version
\usepackage[finalnew,ignoremode]{trackchanges}
\tcignore{\cite}{1}{1}
\tcignore{\autoref}{1}{1}

\begin{document}
\frontmatter      % Begin Roman style (i, ii, iii, iv...) page numbering

%
\UNIVERSITY{{THE UNIVERSITY OF MELBOURNE}}
\university{{The University of Melbourne}}   
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Update your department and school here:
\department{{The Sir Peter MacCallum Department of Oncology}}
\school{{Faculty of Medicine, Dentistry, and Health Sciences}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set up the Title Page
% Change your thesis title and your information here
\title  {Development of new methods for accurate estimation of tumour heterogeneity}
\authors  {\texorpdfstring
            {\href{https://github.com/sebastianhollizeck}{Sebastian Hollizeck\\ \small ORCID: 0000-0002-9504-3497}}
            {Sebastian Hollizeck}
            }
\addresses  {\groupname\\\deptname\\\univname}  % Do not change this here, instead these must be set in the "Thesis.cls" file, please look through it instead
\date       {\today}
\subject    {}
\keywords   {cancer evolution, cancer heterogeneity, ctDNA, variant calling}
\supervisor {Sarah-Jane Dawson, Dineika Chandrananda, Ben Solomon}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\maketitle
%% ----------------------------------------------------------------

\setstretch{1.3}  % It is better to have smaller font and larger line spacing than the other way round

% Define the page headers using the FancyHdr package and set up for one-sided printing
\fancyhead{}  % Clears all page headers and footers
\rhead{\thepage}  % Sets the right side header to show the page number
\lhead{}  % Clears the left side page header



\pagestyle{fancy}  % Finally, use the "fancy" page style to implement the FancyHdr headers

%% ----------------------------------------------------------------
% The Abstract Page
\input{Preamble/Abstract.tex}
\clearpage  % Abstract ended, start a new page

%% ----------------------------------------------------------------
% Declaration Page required for the Thesis, your institution may give you a different text to place here
\input{Preamble/Declaration.tex}
\clearpage  % Declaration ended, now start a new page

%% ----------------------------------------------------------------
% Preface Page required for the Thesis, your institution may give you a different text to place here
\input{Preamble/Preface.tex}
\clearpage  % Preface ended, now start a new page

%% ----------------------------------------------------------------
% The Acknowledgements page, for thanking everyone
\setstretch{1.3}  % Reset the line-spacing to 1.3 for body text (if it has changed)
\input{Preamble/Acknowledgements.tex}
\clearpage  % End of the Acknowledgements
%% ----------------------------------------------------------------

\pagestyle{fancy}  %The page style headers have been "empty" all this time, now use the "fancy" headers as defined before to bring them back
\fancyhead[LO,RE]{}

%% ----------------------------------------------------------------
\fancyhead[LE,RO]{\emph{Contents}}  % Set the left side page header to "Contents"
\tableofcontents  % Write out the Table of Contents

%% ----------------------------------------------------------------
\fancyhead[LE,RO]{\emph{List of Figures}}  % Set the left side page header to "List if Figures"
\listoffigures  % Write out the List of Figures

%% ----------------------------------------------------------------
\fancyhead[LE,RO]{\emph{List of Tables}}  % Set the left side page header to "List of Tables"
\listoftables  % Write out the List of Tables

%%-------------------------------------
\fancyhead[LE,RO]{\emph{List of Equations}}
\addtotoc{List of Equations}
\listofmyequations

\fancyhead[LE,RO]{\emph{List of Listings}}
\addtotoc{List of Listings}
\lstlistoflistings


%% ----------------------------------------------------------------
\setstretch{1.5}  % Set the line spacing to 1.5, this makes the following tables easier to read
\clearpage  % Start a new page
\fancyhead[LE,RO]{\emph{Abbreviations}}
\listofsymbols{ll}  % Include a list of Abbreviations (a table of two columns)
{
% \textbf{Acronym} & \textbf{W}hat (it) \textbf{S}tands \textbf{F}or \\
\textbf{APOBEC} & \textbf{APO}lipoprotein \textbf{B} mRNA \textbf{E}diting enzyme, \textbf{C}atalytic polypeptide-like \\
\textbf{BAM} & \textbf{B}inary \textbf{A}lignment \textbf{M}ap \\
\textbf{bp} & \textbf{b}ase \textbf{p}air\\
\textbf{BQ} & \textbf{B}ase \textbf{Q}uality\\
\textbf{CASCADE} & \textbf{CA}ncer ti\textbf{S}sue \textbf{C}ollection \textbf{A}fter \textbf{DE}ath \\
\textbf{CCF} & \textbf{C}ancer \textbf{C}ell \textbf{Fraction} \\
\textbf{cfDNA} & \textbf{c}ell \textbf{f}ree \textbf{DNA} \\
\textbf{ChIP} & \textbf{Ch}romatin \textbf{I}mmuno\textbf{P}recipitation\\
\textbf{CT} & \textbf{C}omputed \textbf{T}omography \\
\textbf{ctDNA} & \textbf{c}irculating \textbf{t}umour \textbf{DNA}\\
\textbf{DBS} & \textbf{D}ouble \textbf{B}ase \textbf{S}ubstitution \\
\textbf{DNA} & \textbf{D}eoxyribo\textbf{N}ucleic \textbf{A}cid \\
\textbf{F81} & \textbf{F}elsenstein 19\textbf{81} model \\
\textbf{GATK} & \textbf{G}enome \textbf{A}nalysis \textbf{T}ool\textbf{K}it \\
\textbf{HGSOC} & \textbf{H}igh \textbf{G}rade \textbf{S}erous \textbf{O}varian \textbf{C}arcinoma \\
\textbf{HKY85} & \textbf{H}asegawa, \textbf{K}ishino and \textbf{Y}ano 19\textbf{85} model\\
\textbf{HPC} & \textbf{H}igh \textbf{P}erformance \textbf{C}omputing \\
\textbf{H\&E} & \textbf{H}ematoxylin and \textbf{E}osin\\
\textbf{ILM} & \textbf{I}terative \textbf{L}inear \textbf{M}odels \\
\textbf{InDel} & \textbf{In}sertion or \textbf{Del}etion \\
\textbf{LN} & \textbf{L}ymph \textbf{N}ode \\
\textbf{MQ} & \textbf{M}apping \textbf{Q}uality \\
\textbf{MRCA} & \textbf{M}ost \textbf{R}ecent \textbf{C}ommon \textbf{A}ncestor \\
\textbf{NGS} & \textbf{N}ext \textbf{G}eneration \textbf{S}equencing \\
\textbf{NJ} & \textbf{N}eighbour \textbf{J}oining \\
\textbf{NSCLC} & \textbf{N}on-\textbf{S}mall \textbf{C}ell \textbf{L}ung \textbf{C}ancer\\
\textbf{PCA} & \textbf{P}rincipal \textbf{C}omponent \textbf{A}analysis \\
\textbf{PCx} & \textbf{P}rincipal \textbf{C}omponent number x \\
\textbf{PET} & \textbf{P}ositron \textbf{E}mission \textbf{T}omography \\
\textbf{PON} & \textbf{P}anel \textbf{O}f \textbf{N}ormals \\
\textbf{QP} & \textbf{Q}uadratic \textbf{P}rogramming \\
\textbf{RAID} & \textbf{R}edundant \textbf{A}rray of \textbf{I}ndependent \textbf{D}isks \\
\textbf{RNA} & \textbf{R}ibo\textbf{N}ucleic \textbf{A}cid \\
\textbf{ROI} & \textbf{R}egion \textbf{O}f \textbf{I}nterest \\
\textbf{RPRS} & \textbf{R}ead \textbf{P}osition \textbf{R}ank \textbf{S}um \\
\textbf{SBS} & \textbf{S}ingle \textbf{B}ase \textbf{S}ubstitution \\
\textbf{SCLC} & \textbf{S}mall \textbf{C}ell \textbf{L}ung \textbf{C}ancer\\
\textbf{SCT} & \textbf{S}mall \textbf{C}ell \textbf{T}ransformation \\
\textbf{SNP} & \textbf{S}ingle \textbf{N}ucleotide \textbf{P}olymorphism\\
\textbf{SNV} & \textbf{S}ingle \textbf{N}ucleotide \textbf{V}ariant \\
\textbf{SV} & \textbf{S}tructural \textbf{V}ariant \\
\textbf{TAS} & \textbf{T}argeted \textbf{A}mplicon \textbf{S}equencing \\
\textbf{TKI} & \textbf{T}yrosine \textbf{K}inase \textbf{I}nhibitor \\
\textbf{TNBC} & \textbf{T}riple \textbf{N}egative \textbf{B}reast \textbf{C}ancer \\
\textbf{UPGMA} & \textbf{U}nweighted \textbf{P}air \textbf{G}roup \textbf{M}ethod with \textbf{A}rithmetic mean \\
\textbf{UV} & \textbf{U}ltra \textbf{V}iolet light\\
\textbf{VCF} & \textbf{V}ariant \textbf{C}all \textbf{F}ormat\\
\textbf{VEP} & \textbf{V}ariant \textbf{E}ffect \textbf{P}redictor \\
\textbf{WES} & \textbf{W}hole \textbf{E}xome \textbf{S}equencing\\
\textbf{WGD} & \textbf{W}hole \textbf{G}enome \textbf{D}oubling \\
\textbf{WGS} & \textbf{W}hole \textbf{G}enome \textbf{S}equencing\\
\textbf{WPGMA} & \textbf{W}eighted \textbf{P}air \textbf{G}roup \textbf{M}ethod with \textbf{A}rithmetic mean \\

}
% currently sorted
%\todo[inline, color=red]{Sort abbrvs alphabetically}


%% ----------------------------------------------------------------
%\clearpage  % Start a new page
%\lhead{\emph{Constants}}  % Set the left side page header to "Physical Constants"
%\listofconstants{lrcl}  % Include a list of Physical Constants (a four column table)
%{
%% Constant Name & Symbol & = & Constant Value (with units) \%\
%Speed of Light & $c$ & $=$ & $2.997\ 924\ 58\times10^{8}\ \mbox{ms}^{-\mbox{s}}$ (exact)\\
%
%}

%% ----------------------------------------------------------------
%\clearpage  %Start a new page
%\lhead{\emph{Symbols}}  % Set the left side page header to "Symbols"
%\listofnomenclature{lll}  % Include a list of Symbols (a three column table)
%{
%% symbol & name & unit \\
%$a$ & distance & m \\
%$P$ & power & W (Js$^{-1}$) \\
%& & \\ % Gap to separate the Roman symbols from the Greek
%$\omega$ & angular frequency & rads$^{-1}$ \\
%}
%% ----------------------------------------------------------------
% End of the pre-amble, contents and lists of things


%% ----------------------------------------------------------------
\mainmatter	  % Begin normal, numeric (1,2,3...) page numbering
\pagestyle{fancy}  % Return the page headers back to the "fancy" style

%setup so that the header shows the chapter and the footer shows the page number
\fancyhead[RO,LE]{\leftmark}
%\fancyhead[LE]{\leftmark}
\fancyhead[RE,LO]{\rightmark}
\fancyfoot[LE,RO]{\thepage}
\fancyfoot[RE,LO]{}

%make pretty lines
%\renewcommand{\footrulewidth}{1pt}
\renewcommand{\headrulewidth}{1pt}

%change the distance of the number to the top of the page
\renewcommand{\chapterheadstartvskip}{\vspace*{-4\baselineskip}}

% Include the chapters of the thesis, as separate files
% Just uncomment the lines as you write the chapters

\input{Chapters/Introduction/main-Introduction.tex} 

\input{Chapters/Variantcalling/main-Variantcalling.tex}  

\input{Chapters/CASCADE/main-CASCADE.tex} 

\input{Chapters/Mismatchfinder/main-Mismatchfinder.tex} 

\input{Chapters/Conclusion/main-Conclusion.tex} % 

%% ----------------------------------------------------------------
% Now begin the Appendices, including them as separate files
%clear all floats etc
%\afterpage{\cleardoublepage}
\cleardoublepage


%\backmatter

%% ----------------------------------------------------------------
\label{Bibliography}
\fancyhead[LE,RO]{Bibliography}  % Change the left side page header to "Bibliography"
\fancyhead[LO,RE]{}
\printbibliography


\cleardoublepage
\addtocontents{toc}{\vspace{2em}}  % Add a gap in the Contents, for aesthetics
\addtocontents{lof}{\vspace{2em}}
\addtocontents{lol}{\vspace{10pt}}

\appendix % Cue to tell LaTeX that the following 'chapters' are Appendices
\addappheadtotoc % add an entry to the TOC
%\addtocontents{lof}{\protect\mbox{}\protect\hrulefill\par} % line between normal figures and appendix
\addcontentsline{lof}{chapter}{Appendices}
\appendixpage % add a seperation page (which we redesigned)


\fancyhead[RO,LE]{\leftmark}
%\fancyhead[LE]{\leftmark}
\fancyhead[RE,LO]{\rightmark}
\fancyfoot[LE,RO]{\thepage}
\fancyfoot[RE,LO]{}



\input{Appendices/Variantcalling/app-main.tex}	% Appendix Title

\input{Appendices/CASCADE/app-main.tex}

\input{Appendices/Mismatchfinder/app-main.tex}

%\input{Appendices/AppendixB} % Appendix Title

%\input{Appendices/AppendixC} % Appendix Title





\end{document}  % The End
%% ----------------------------------------------------------------