diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java new file mode 100644 index 000000000..4541a0537 --- /dev/null +++ b/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] + * + *
+ * [Functionality of this walker] + *
+ * + *+ * [Input description] + *
+ * + *+ * [Output description] + *
+ * + *+ * java + * -jar GenomeAnalysisTK.jar + * -T $WalkerName + *+ * + * @author Your Name + * @since Date created + */ +public class GATKDocsExample extends RodWalker