56 lines
2.5 KiB
Markdown
56 lines
2.5 KiB
Markdown
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## Writing GATKdocs for your walkers
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http://gatkforums.broadinstitute.org/gatk/discussion/1324/writing-gatkdocs-for-your-walkers
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<p>The GATKDocs are what we call <a href="http://www.broadinstitute.org/gatk/gatkdocs/">"Technical Documentation"</a> in the Guide section of this website. The HTML pages are generated automatically at build time from specific blocks of documentation in the source code. </p>
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<p>The best place to look for example documentation for a GATK walker is GATKDocsExample walker in <code>org.broadinstitute.sting.gatk.examples</code>. This is available <a href="https://github.com/broadgsa/gatk/blob/master/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java">here</a>. </p>
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<p>Below is the reproduction of that file from August 11, 2011:</p>
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<pre><code class="pre_md">/**
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* [Short one sentence description of this walker]
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*
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* <p>
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* [Functionality of this walker]
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* </p>
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*
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* <h2>Input</h2>
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* <p>
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* [Input description]
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* </p>
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*
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* <h2>Output</h2>
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* <p>
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* [Output description]
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* </p>
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*
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* <h2>Examples</h2>
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* PRE-TAG
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* java
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* -jar GenomeAnalysisTK.jar
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* -T $WalkerName
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* PRE-TAG
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*
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* @category Walker Category
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* @author Your Name
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* @since Date created
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*/
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public class GATKDocsExample extends RodWalker<Integer, Integer> {
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/**
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* Put detailed documentation about the argument here. No need to duplicate the summary information
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* in doc annotation field, as that will be added before this text in the documentation page.
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*
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* Notes:
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* <ul>
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* <li>This field can contain HTML as a normal javadoc</li>
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* <li>Don't include information about the default value, as gatkdocs adds this automatically</li>
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* <li>Try your best to describe in detail the behavior of the argument, as ultimately confusing
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* docs here will just result in user posts on the forum</li>
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* </ul>
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*/
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@Argument(fullName="full", shortName="short", doc="Brief summary of argument [~ 80 characters of text]", required=false)
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private boolean myWalkerArgument = false;
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; }
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public Integer reduceInit() { return 0; }
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public Integer reduce(Integer value, Integer sum) { return value + sum; }
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public void onTraversalDone(Integer result) { }
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}</code class="pre_md"></pre>
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