All info from the user manual is now in the wiki. Deleting.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1124 348d0f76-0448-11de-a6fe-93d51630548a

doc/GATK_User_Manual.tex

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-\documentclass[11pt,fullpage]{article}
-\usepackage[urlcolor=blue,colorlinks=true]{hyperref}
-
-\oddsidemargin 0.0in
-\textwidth 6.5in
-
-\begin{document}
-
-\title{Genome Analysis Toolkit (GATK) User Manual}
-\author{Matt Hanna}
-\date{30 Mar 2009}
-\maketitle
-
-\section{Walkers}
-\subsection{Command-line Arguments}
-Users can create command-line arguments for walkers by creating public
-member variables annotated with @Argument in the walker.  The
-@Argument annotation takes a number of different parameters:
-
-\begin{enumerate}
-  \item [fullName] The full name of this argument.  Defaults to the
-    toLowerCase()'d member name.  When specifying fullName on the 
-    command line, prefix a double dash (--).
-  \item [shortName] The alternate, short name for this argument.
-    Defaults to the first letter of the member name.  When specifying 
-    shortName on the command line, prefix a single dash (-).
-  \item [doc] Documentation for this argument.  Will appear in help
-    output when a user either requests help with the --help (-h)
-    argument or when a user specifies an invalid set of arguments.
-  \item [required] Whether the argument is required when used with
-    this walker.  Default is required = true.
-  \item [exclusive] Specifies that this argument is mutually
-    exclusive of another argument in the same walker.  Defaults to not
-    mutually exclusive of any other arguments.
-  \item [defaultValue] Specifies the default value for this parameter,
-    in string form.  
-\end{enumerate}
-
-\subsubsection{Passing Command-line Arguments}
-Arguments can be passed to the walker using either the full name or
-the short name.  If passing arguments using the full name, the syntax
-is $--$$<$arg full name$>$ $<$value$>$.
-\begin{verbatim}
---myint 6
-\end{verbatim}
-
-If passing arguments using the short name,
-the syntax is -$<$arg short name$>$$<$value$>$.  Note that there is no space
-between the short name and the value:
-\begin{verbatim}
--m6
-\end{verbatim}
-
-Boolean (class) and boolean (primitive) arguments are a special in
-that they require no argument.  The presence of a boolean indicates
-true, and its absence indicates false.  The following example sets a
-flag to true.
-\begin{verbatim}
--B
-
-\end{verbatim}
-
-\subsubsection{Examples}
-
-Create an required int parameter with full name --myint, short name
--m.
-Pass this argument by adding ``--myint 6'' or -m6 to the command line.
-\begin{verbatim}
-import org.broadinstitute.sting.utils.cmdLine.Argument;
-
-public class HelloWalker extends ReadWalker<Integer,Long> {
-    @Argument
-    public int myInt;
-\end{verbatim}
-
-Create an optional float parameter with full name
---myFloatingPointArgument, short name -m.  Pass this argument by
-adding --myFloatingPointArgument 2.71 or -m2.71.
-\begin{verbatim}
-import org.broadinstitute.sting.utils.cmdLine.Argument;
-
-public class HelloWalker extends ReadWalker<Integer,Long> {
-    @Argument(fullName="myFloatingPointArgument",required=false,defaultValue="3.14159")
-    public float myFloat;
-\end{verbatim}
-
-The GATK will parse the argument differently depending on the type of
-the public member variable's type.  Many different argument types are 
-supported, including primitives and their wrappers, arrays, typed and 
-untyped collections, and any type with a String constructor.
-
-When the GATK cannot completely infer the type (such as in the case of
-untyped collections), it will assume that the argument is a String.
-GATK is aware of concrete implementations of some interfaces and
-abstract classes.  If the argument's member variable is of type List
-or Set, the GATK will fill the member variable with a concrete
-ArrayList or TreeSet, respectively.  Maps are not currently supported.
-
-\subsection{Output}
-By default, the walkers provide protected out and err PrintStreams.
-Users can write to these streams just as they write to System.out and
-System.err.  This output can be redirected to a file using the out,
-err, and outerr command-line arguments.
-
-\subsection{Logging}
-The walkers provide a protected logger instance.  Users can adjust the
-debug level of the walkers using the -l command line option.
-
-Turning on verbose logging can produce more output than the user
-really needs.  To selectively turn on logging for a class or package,
-the user can specify a log4j.properties property file from the command
-line as follows:
-
-\begin{verbatim}
--Dlog4j.configuration=file:///humgen/gsa-scr1/hanna/src/Sting/java/config/log4j.properties
-\end{verbatim}
-
-An example log4j.properties file is available in the java/config
-directory of the subversion repository.
-
-\end{document}