Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java

@@ -0,0 +1,82 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.examples;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
+import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+
+/**
+ * [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>
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T $WalkerName
+ *  </pre>
+ *
+ * @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) { }
+}