A dumping ground for information that will eventually become the GATK user manual. Currently has basic information about command-line arguments and walker output streams.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@223 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.
+\end{enumerate}
+
+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.
+
+\end{document}