diff --git a/doc/GATK_User_Manual.pdf b/doc/GATK_User_Manual.pdf index 24bf683fd..a8bb44092 100644 Binary files a/doc/GATK_User_Manual.pdf and b/doc/GATK_User_Manual.pdf differ diff --git a/doc/GATK_User_Manual.tex b/doc/GATK_User_Manual.tex index 295d90979..277b96012 100755 --- a/doc/GATK_User_Manual.tex +++ b/doc/GATK_User_Manual.tex @@ -32,8 +32,28 @@ member variables annotated with @Argument in the walker. The \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} +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} +@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} +@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