GATKdocs

The documentation itself

• Released version: [1]
• Stable version including private code (Broad only): [2]
• Unstable, development version, including private code (Broad only): [3]

Note that the Released and Stable version will not be available until GATK 1.2 release.

Writing GATKdocs for your walkers

The best place to look for example documentation for a GATK walker is GATKDocsExample walker in org.broadinstitute.sting.gatk.examples. This will be available as of GATK 1.2 at [4]. The resulting GATKdoc can be seen at:

GATKDoc of GATKDocsExample in stable or GATKDoc of GATKDocsExample in unstable

Below is the reproduction of that file from August 11, 2011:

/**
 * [Short one sentence description of this walker]
 *
 * <p>
 * [Functionality of this walker]
 * </p>
 *
 * <h2>Input</h2>
 * <p>
 * [Input description]
 * </p>
 *
 * <h2>Output</h2>
 * <p>
 * [Output description]
 * </p>
 *
 * <h2>Examples</h2>
 * PRE-TAG
 *    java
 *      -jar GenomeAnalysisTK.jar
 *      -T $WalkerName
 * PRE-TAG
 *
 * @author Your Name
 * @since Date created
 */
public class GATKDocsExample extends RodWalker<Integer, Integer> {
    /**
     * Put detailed documentation about the argument here.  No need to duplicate the summary information
     * in doc annotation field, as that will be added before this text in the documentation page.
     *
     * Notes:
     * <ul>
     *     <li>This field can contain HTML as a normal javadoc</li>
     *     <li>Don't include information about the default value, as gatkdocs adds this automatically</li>
     *     <li>Try your best to describe in detail the behavior of the argument, as ultimately confusing
     *          docs here will just result in user posts on the forum</li>
     * </ul>
     */
    @Argument(fullName="full", shortName="short", doc="Brief summary of argument [~ 80 characters of text]", required=false)
    private boolean myWalkerArgument = false;

    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; }
    public Integer reduceInit() { return 0; }
    public Integer reduce(Integer value, Integer sum) { return value + sum; }
    public void onTraversalDone(Integer result) { }
}