76 lines
2.9 KiB
TeX
Executable File
76 lines
2.9 KiB
TeX
Executable File
\documentclass[11pt,fullpage]{article}
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\usepackage[urlcolor=blue,colorlinks=true]{hyperref}
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\oddsidemargin 0.0in
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\textwidth 6.5in
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\begin{document}
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\title{Genome Analysis Toolkit (GATK) User Manual}
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\author{Matt Hanna}
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\date{30 Mar 2009}
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\maketitle
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\section{Walkers}
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\subsection{Command-line Arguments}
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Users can create command-line arguments for walkers by creating public
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member variables annotated with @Argument in the walker. The
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@Argument annotation takes a number of different parameters:
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\begin{enumerate}
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\item [fullName] The full name of this argument. Defaults to the
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toLowerCase()'d member name. When specifying fullName on the
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command line, prefix a double dash (--).
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\item [shortName] The alternate, short name for this argument.
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Defaults to the first letter of the member name. When specifying
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shortName on the command line, prefix a single dash (-).
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\item [doc] Documentation for this argument. Will appear in help
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output when a user either requests help with the --help (-h)
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argument or when a user specifies an invalid set of arguments.
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\item [required] Whether the argument is required when used with
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this walker. Default is required = true.
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\item [exclusive] Specifies that this argument is mutually
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exclusive of another argument in the same walker. Defaults to not
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mutually exclusive of any other arguments.
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\item [defaultValue] Specifies the default value for this parameter,
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in string form.
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\end{enumerate}
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Examples:
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Create an required int parameter with full name --myint, short name
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-m.
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Pass this argument by adding ``--myint 6'' or -m6 to the command line.
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\begin{verbatim}
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@Argument
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public int myInt;
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\end{verbatim}
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Create an optional float parameter with full name
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--myFloatingPointArgument, short name -m. Pass this argument by
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adding --myFloatingPointArgument 2.71 or -m2.71.
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\begin{verbatim}
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@Argument(fullName="myFloatingPointArgument",required=false,defaultValue="3.14159")
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public float myFloat;
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\end{verbatim}
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The GATK will parse the argument differently depending on the type of
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the public member variable's type. Many different argument types are
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supported, including primitives and their wrappers, arrays, typed and
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untyped collections, and any type with a String constructor.
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When the GATK cannot completely infer the type (such as in the case of
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untyped collections), it will assume that the argument is a String.
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GATK is aware of concrete implementations of some interfaces and
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abstract classes. If the argument's member variable is of type List
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or Set, the GATK will fill the member variable with a concrete
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ArrayList or TreeSet, respectively. Maps are not currently supported.
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\subsection{Output}
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By default, the walkers provide protected out and err PrintStreams.
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Users can write to these streams just as they write to System.out and
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System.err. This output can be redirected to a file using the out,
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err, and outerr command-line arguments.
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\end{document}
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