## 1. Analysis output overview

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.

## 2. PrintStream

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:

out.println("Hello, world!");

By default, @Output streams prepopulate fullName, shortName, required, and doc. 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 System.out.

If your walker outputs a custom format that requires more than simple concatenation by [Queue]() you should also implement a custom Gatherer.

## 3. SAMFileWriter

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 SAMFileReader or 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.

## 4. VCFWriter

VCFWriter outputs behave similarly to PrintStreams and SAMFileWriters. Declare a VCFWriter as follows:

@Output(doc="File to which variants should be written",required=true) protected VCFWriter writer = null;

## 5. Debugging Output

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

An example log4j.properties file is available in the java/config directory of the Git repository.