SCarborSNV_Paper/main.tex at master · coldham10/SCarborSNV_Paper · GitHub

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\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage{subfiles}
\usepackage[margin=1in]{geometry}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{graphicx}
\usepackage{tikz}
\usepackage{subcaption}
\usepackage{setspace}
\usepackage{algorithm}
\usepackage{algpseudocode}
\usepackage[font=small, width=\textwidth,margin=3em]{caption}
\usepackage{cite}

\newcommand{\norm}[1]{\left\lVert#1\right\rVert}
\renewcommand{\thealgorithm}{:}


\begin{document}
\nocite{*}

\pagenumbering{roman}

\subfile{titlepage}
\doublespacing
\setcounter{page}{2}
\subfile{sections/abstract}

\tableofcontents

\newpage
\setcounter{page}{1}
\pagenumbering{arabic}

\section{Introduction}
\subfile{sections/introduction}

\section{Methods}
\subfile{sections/methods}

\section{Results}
\subfile{sections/results}

\section{Discussion}
\subfile{sections/discussion}


\section{Software availability}
SCarborSNV has been implemented in C and is available at \texttt{https://github.com/coldham10/SCarborSNV}.
The SCarborSNV source has been licensed under the GNU General Public License, Version 3.

%TODO near eqns 13, 14 instead of reffering to phasing so heavily, instead beter to show probability of an unphased genotype vector given \sigma, refer to Li, statistical framework for SNP calling...


\newpage
\bibliography{SCarborSNV}
\bibliographystyle{unsrt}

\newpage
\appendix
\subfile{sections/appendix}


\end{document}

%After done with algorithm: simulator! Real data results, efficiency comparison, introduction and discussion... Poster? Style, change from we to factual voice? dbSNP and missing data?? Account for different read depths? likelihood for single read much greater than that for multi: so maybe normalize each?