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In theory, any class implementing the
OutputStream interface. In practice, three types of classes are commonly used:
PrintStreams for plain text files,
SAMFileWriters for BAM files, and
VCFWriters for VCF files.
To declare a basic
PrintStream for output, use the following declaration syntax:
@Output public PrintStream out;
And use it just as you would any other PrintStream:
@Output streams prepopulate
required in this context means that the GATK will always fill in the contents of the
out field for you. If the user specifies no
--out command-line argument, the 'out' field will be prepopulated with a stream pointing to
If your walker outputs a custom format that requires more than simple concatenation by Queue you should also implement a custom
For some applications, you might need to manage their own SAM readers and writers directly from inside your walker. Current best practice for creating these Readers / Writers is to declare arguments of type
SAMFileWriter as in the following example:
@Output SAMFileWriter outputBamFile = null;
If you do not specify the full name and short name, the writer will provide system default names for these arguments. Creating a
SAMFileWriter in this way will create the type of writer most commonly used by members of the GSA group at the Broad Institute -- it will use the same header as the input BAM and require presorted data. To change either of these attributes, use the
StingSAMIterator interface instead:
@Output StingSAMFileWriter outputBamFile = null;
and later, in
initialize(), run one or both of the following methods:
You can change the header or presorted state until the first alignment is written to the file.
VCFWriter outputs behave similarly to
SAMFileWriters. Declare a
VCFWriter as follows:
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter writer = null;
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 is really necessary. To selectively turn on logging for a class or package, specify a
log4j.properties property file from the command line as follows:
-Dlog4j.configuration=file:///<your development root>/Sting/java/config/log4j.properties
log4j.properties file is available in the
java/config directory of the Git repository.