appendix1.tex

%hack to change the last header on the TOC to say APPENDIX
% \addtocontents{toc}{\protect\clearpage\lhead[APPENDIX]{APPENDIX}}
\addtocontents{toc}{\protect\afterpage{\lhead[APPENDIX]{APPENDIX}}}

\chapter{Code to Reproduce Analyses in Appendix~\protect\structuredref{}}
\label{ch:structured_code}
\newpage
\inputminted[breaklines, breakanywhere, tabsize=2]{Makefile}{ch3/scripts/ch3_makefiles.txt}

\chapter{Code to Reproduce Analyses in Chapter~\protect\kbbqref{}}
\label{ch:kbbq_plot_code}
\newpage
\section{Data Analysis Code}
\inputminted[breaklines, breakanywhere, tabsize=2]{Makefile}{ch4/scripts/ch4_makefiles.txt}
\section{Code to Generate Plots}
\inputminted[breaklines, breakanywhere, tabsize=2]{r}{ch4/scripts/plot_benchmarks.R}
\inputminted[breaklines, breakanywhere, tabsize=2]{r}{defense/recalibration_explainer.R}

\chapter{KBBQ Program Code}
\label{ch:kbbq_code}
\newpage
\section{Headers}
\inputminted[breaklines, breakanywhere, tabsize=2]{cpp}{ch4/scripts/kbbq_include.hh}
\section{Source}
\inputminted[breaklines, breakanywhere, tabsize=2]{cpp}{ch4/scripts/kbbq_src.cc}

\chapter{Code to Reproduce Analyses in Chapter~\protect\evaluatingref{}}
\label{ch:evaluating_code}
\newpage
\section{Code to Call Variants With CHM1-CHM13 Data}
\inputminted[breaklines, breakanywhere, tabsize=2]{Makefile}{ch5/scripts/chm1-chm13_variants_makefiles.txt}
\section{Code to Call Variants With Simulated Data}
\inputminted[breaklines, breakanywhere, tabsize=2]{Makefile}{ch5/scripts/sim_variants_makefiles.txt}
\section{Code to Call Variants With \textit{E. melliodora} Data}
\inputminted[breaklines, breakanywhere, tabsize=2]{Makefile}{ch5/scripts/euc_variants_makefiles.txt}
\section{ROC Plotting Code}
\inputminted[breaklines, breakanywhere, tabsize=2]{r}{ch5/scripts/roc_plots.R}
\section{Summary Plotting Code}
\inputminted[breaklines, breakanywhere, tabsize=2]{r}{ch5/scripts/hapdip_summary_plots.R}