Made the coverage slides compilable.

lectures/coverage/coverage.tex

-% Alter these four lines for a new presentation.
-\providecommand{\me}{Jeroen F. J. Laros}
-\providecommand{\myTitle}{Copy Number of Substrings}
+\documentclass[slidestop]{beamer}
+
+\title{Copy Number of Substrings}
 \providecommand{\myConference}{Work discussion}
 \providecommand{\myDate}{Tuesday, 13 October 2009}
-
-% Now go to %%% BEGIN PRESENTATION %%%
-
-\documentclass[a4, portrait]{seminar}
-
-\usepackage{semcolor} % For coloured text.
-\usepackage{slidesec} % For section headings.
-\usepackage{newcent}  % This is a better font for presentations.
-\input{seminar.bug}
-
-\usepackage{graphicx} % For pictures.
-\usepackage{fancybox} % For the background picture.
-
-\definecolor{Blue}{rgb}{0.,0.11372,0.37647} % Custom LUMC color
-
-\renewcommand{\labelitemi}{\textcolor{white}{$\bullet$}} % Make the bullets for
-\renewcommand{\labelitemii}{\textcolor{white}{--}}       % itemising white.
-\renewcommand{\labelitemiii}{\textcolor{white}{$\ast$}}
-\renewcommand{\labelitemiv}{\textcolor{white}{$\circ$}}
-
-\newslideframe{TITLE}{ % Template for the title.
-  \boxput{
-    \rput(0, 0){\includegraphics[angle=90, scale=.485]{bg}}
-  }{#1}
-}
-
-\newslideframe{PRES}{ % Template for the body.
-  \boxput{
-    \rput(0, 0){\includegraphics[angle=90, scale=.485]{bg2}}
-  }{
-    \textcolor{Blue}{
-    \rput[l]{90}(8.57, -1.5){\scriptsize{\myConference}} 
-    \rput[c]{90}(8.57, 5.35){\scriptsize{\theslide/\pageref{LastPage}}}
-    \rput[r]{90}(8.57, 12.2){\scriptsize{\myDate}}
-    }
-    \white #1
+\author{Jeroen F. J. Laros}
+\providecommand{\myGroup}{}
+\providecommand{\myDepartment}{Department of Human Genetics}
+\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+\providecommand{\lastCenterLogo}{
+  \raisebox{-0.1cm}{
+    %\includegraphics[height = 1cm]{lgtc_logo}
+    %\includegraphics[height = 0.7cm]{ngi_logo}
   }
 }
-
-\renewcommand{\makeslideheading}[1]{ % Put the slide headings on top.
-  \rput[l](0.2, .40){
-      \textbf{
-        \textcolor{Blue}{#1}
-    }
-  }
-  \newline
+\providecommand{\lastRightLogo}{
+  %\includegraphics[height = 0.7cm]{nbic_logo}
+  %\includegraphics[height = 0.8cm]{nwo_logo_en}
+  \hspace{1.5cm}\includegraphics[height = 0.7cm]{gen2phen_logo}
 }
 
-\pagestyle{empty}
+\usetheme{lumc}
 
 \begin{document}
 
-\slideframe{TITLE} % Use the title template.
-
-\begin{slide}
-\setcounter{slide}{0}
-\vspace*{1.5cm}
-\begin{center}
-{\bf\Large{\myTitle}}\\
-\vspace{2.5cm}
-\textcolor{Blue}{
-  {\bf
-    \small{\me}\\
-    \small{Department of Human Genetics}\\
-    \small{Center for Human and Clinical Genetics}
-  }
-}
-\end{center}
-\vfill
-\end{slide}
-
-\slideframe{PRES} % Use the body template.
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
 
-%%% BEGIN PRESENTATION %%%
+% Make the title page.
+\bodytemplate
 
-\begin{slide}
-\slideheading{Problem description}
+% First page of the presentation.
+\begin{frame}
+\frametitle{Problem description}
 
 A sequenced string is usually mapped back to a reference genome.
 
@@ -94,10 +46,10 @@ is not unique increases when the length decreases.
 \item Map everything randomly on one of the occurrences.
 \end{itemize}
 \vfill
-\end{slide}
+\end{frame}
 
-\begin{slide}
-\slideheading{Taking notice of the problem}
+\begin{frame}
+\frametitle{Taking notice of the problem}
 By analysing the reference genome itself, we can predict how many times each
 read occurs.
 
@@ -111,7 +63,9 @@ count number.
 \item 
 \item Verification in general.
 \end{itemize}
+\end{frame}
 
+\begin{frame}
 \begin{center}
 \fbox{
 \scalebox{0.7}{
@@ -120,10 +74,10 @@ count number.
 }
 \end{center}
 \vfill
-\end{slide}
+\end{frame}
 
-\begin{slide}
-\slideheading{Practical solution}
+\begin{frame}
+\frametitle{Practical solution}
 Preliminary research [Rietveld 2009] showed that indexing the entire human 
 genome can be done efficiently (half an hour). With non-dedicated hardware
 and low memory capabilities about eight hours.
@@ -131,13 +85,12 @@ and low memory capabilities about eight hours.
 Output consists of a truncated-suffix array (suffixes truncated at any length),
 this array can be used to determine all occurrences of...
 \vfill
-\end{slide}
+\end{frame}
 
-\begin{slide}
-\rput(11.4,0.6){\includegraphics[scale=0.1]{Gen2Phen}}
-\slideheading{Questions?}
+\lastpagetemplate
+\begin{frame}
+\frametitle{Questions?}
 \vfill
-\label{LastPage}
-\end{slide}
+\end{frame}
 
 \end{document}

presentation @ 67af7908

-Subproject commit ef45a090b15f92d6aacd073fa8955e27230bd83a
+Subproject commit 67af7908862139e1dc4c966e1dcd984d2db0592b