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-\documentclass[11pt,fullpage]{article}
-\usepackage[urlcolor=blue,colorlinks=true]{hyperref}
-
-\oddsidemargin 0.0in
-\textwidth 6.5in
-
-\begin{document}
-
-\title{Getting Started with the Genome Analysis Toolkit (GATK)}
-\author{Matt Hanna}
-\date{Created March 16, 2009\\ Updated \today}
-\maketitle
-
-\section{Build Prerequisites}
-GATK requires JDK 1.6 and Ant 1.7.1 to compile.
-
-\section{Getting and Building the Source}
-GATK is located in the Sting svn repository, and
-compiles using a build.xml in the root directory.
-
-Download and build the source as follows:
-\begin{verbatim}
-  svn co https://svnrepos/Sting/trunk Sting
-  cd Sting
-  ant
-\end{verbatim}
-
-\section{Getting Started}
-The core concept behind GATK is the walker, a class that implements the 
-three core operations: filtering, mapping, and reducing.
-
-\begin{description}
-  \item [filter] reduces the size of the dataset by applying a predicate.  
-  \item [map] Applies a function to each individual element in a dataset, 
-    effectively 'mapping' it to a new element.
-  \item [reduce] Inductively combines the elements of a list.  The base
-    case is supplied by the reduceInit() function, and the inductive step
-    is performed by the reduce() function.
-\end{description}
-Users of the GATK will provide a walker to run their analyses.  The engine
-will produce a result by first filtering the dataset, running a map operation,
-and finally reducing the map operation to a single result.  
-
-\section{Creating a Walker}
-To be loaded by GATK, the walker must satisfy the following properties:
-\begin{enumerate}
-  \item It must be a loose class, not packaged into a jar file.
-  \item It must be in the unnamed package (in other words, the source
-    should not start with a package declaration).
-  \item It must subclass one of the basic walkers in the 
-    org.broadinstitute.sting.gatk.walkers package: ReadWalker or 
-    LociWalker.
-  \item It must live in the directory \$STING\_HOME/dist/walkers.
-\end{enumerate}
-
-\section{Example}
-This walker will print output for each read it sees, eventually computing the
-total number of reads by mapping every read to 1 and summing all the 1s to
-realize the total number of reads.
-
-\begin{samepage}
-Copy the following text into the file \$STING\_HOME/dist/walkers/HelloWalker.java:
-
-\begin{verbatim}
-import net.sf.samtools.SAMRecord;
-
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-
-/**
- * Define a class extending from ReadWalker with types
- * <MapType,ReduceType>.  
- */
-public class HelloWalker extends ReadWalker<Integer,Long> {
-    private Long currentRead = 0L;
-
-    // Maps each read to the value 1.
-    public Integer map(LocusContext context, SAMRecord read) {
-        System.out.printf("Hello read %d%n", ++currentRead );
-        return 1; 
-    }
-
-    // Provides an initial value for the reduce function.
-    public Long reduceInit() { return 0L; }
-    
-    // Defines how to compute the reduction given a value in the list. 
-    public Long reduce(Integer value, Long sum) { 
-        return sum + value;
-    }
-}
-\end{verbatim}
-\end{samepage}
-To compile the walker:
-\begin{verbatim}
-setenv CLASSPATH $STING_HOME/dist/GenomeAnalysisTK.jar:$STING_HOME/dist/sam-1.0.jar
-javac HelloWalker.java
-\end{verbatim}
-To run the walker:
-\begin{verbatim}
-mkdir $STING_HOME/dist/walkers
-java -Xmx4096m -jar dist/GenomeAnalysisTK.jar \
-     -R/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta \
-     -I /broad/1KG/legacy_data/trio/na12878.bam -T Hello \
-     -L chr1:10000000-10000100 -l WARN
-\end{verbatim}
-This command will run the walker across a subsection of chromosome 1, operating on 
-reads which align to that subsection.  If you'd like to see more information from the GATK 
-on what it's doing, you can change the logging level (-l) to INFO.
-
-\end{document}