Merge pull request #705 from broadinstitute/gg_simplify_gatkdocs_templates
Changed the GATKDocs format to PHP
This commit is contained in:
Eric Banks
commit
fe86dafc41
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@ -72,7 +72,7 @@ public abstract class DocumentedGATKFeatureHandler {
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* @return
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*/
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public String getDestinationFilename(ClassDoc doc, Class clazz) {
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return GATKDocUtils.htmlFilenameForClass(clazz);
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return GATKDocUtils.phpFilenameForClass(clazz);
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}
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/**
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@ -40,7 +40,7 @@ public class GATKDocUtils {
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public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
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/**
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* Return the filename of the GATKDoc HTML that would be generated for Class. This
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* Return the filename of the GATKDoc PHP that would be generated for Class. This
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* does not guarantee that the docs exist, or that docs would actually be generated
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* for class (might not be annotated for documentation, for example). But if
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* this class is documented, GATKDocs will write the docs to a file named as returned
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@ -49,8 +49,8 @@ public class GATKDocUtils {
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* @param c
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* @return
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*/
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public static String htmlFilenameForClass(Class c) {
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return c.getName().replace(".", "_") + ".html";
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public static String phpFilenameForClass(Class c) {
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return c.getName().replace(".", "_") + ".php";
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}
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/**
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@ -61,7 +61,7 @@ public class GATKDocUtils {
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* @return
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*/
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public static String helpLinksToGATKDocs(Class c) {
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String classPath = htmlFilenameForClass(c);
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String classPath = phpFilenameForClass(c);
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StringBuilder b = new StringBuilder();
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b.append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath);
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//b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
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@ -205,9 +205,6 @@ public class GATKDoclet {
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try {
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// basic setup
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destinationDir.mkdirs();
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FileUtils.copyFile(new File(settingsDir + "/bootstrap.min.css"), new File(destinationDir + "/bootstrap.min.css"));
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FileUtils.copyFile(new File(settingsDir + "/bootstrap.min.js"), new File(destinationDir + "/bootstrap.min.js"));
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FileUtils.copyFile(new File(settingsDir + "/jquery.min.js"), new File(destinationDir + "/jquery.min.js"));
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// print the Version number
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FileUtils.writeByteArrayToFile(new File(destinationDir + "/current.version.txt"), getSimpleVersion(absoluteVersion).getBytes());
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@ -383,7 +380,7 @@ public class GATKDoclet {
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}
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/**
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* Create the html index listing all of the GATKDocs features
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* Create the php index listing all of the GATKDocs features
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*
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* @param cfg
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* @param indexData
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@ -394,7 +391,7 @@ public class GATKDoclet {
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Template temp = cfg.getTemplate("generic.index.template.html");
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/* Merge data-model with template */
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Writer out = new OutputStreamWriter(new FileOutputStream(new File(destinationDir + "/index.html")));
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Writer out = new OutputStreamWriter(new FileOutputStream(new File(destinationDir + "/index.php")));
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try {
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temp.process(groupIndexData(indexData), out);
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out.flush();
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@ -404,7 +401,7 @@ public class GATKDoclet {
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}
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/**
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* Helpful function to create the html index. Given all of the already run GATKDocWorkUnits,
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* Helpful function to create the php index. Given all of the already run GATKDocWorkUnits,
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* create the high-level grouping data listing individual features by group.
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*
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* @param indexData
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@ -566,7 +566,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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// make hashmap of simplename and url
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final HashMap<String, Object> nugget = new HashMap<String, Object>();
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nugget.put("name", filter.getSimpleName());
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nugget.put("filename", GATKDocUtils.htmlFilenameForClass(filter));
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nugget.put("filename", GATKDocUtils.phpFilenameForClass(filter));
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bucket.add(nugget);
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}
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}
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@ -863,7 +863,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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List<String> rodTypes = new ArrayList<String>();
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for (FeatureManager.FeatureDescriptor descriptor : manager.getByFeature(featureClass)) {
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rodTypes.add(String.format("<a href=%s>%s</a>",
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GATKDocUtils.htmlFilenameForClass(descriptor.getCodecClass()),
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GATKDocUtils.phpFilenameForClass(descriptor.getCodecClass()),
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descriptor.getName()));
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}
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@ -28,7 +28,7 @@ package org.broadinstitute.gatk.utils.help;
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public class HelpConstants {
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public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk";
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public final static String GATK_DOCS_URL = BASE_GATK_URL + "/gatkdocs/";
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public final static String GATK_DOCS_URL = BASE_GATK_URL + "/tooldocs/";
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public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/";
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public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
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@ -37,7 +37,7 @@ public class HelpConstants {
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*/
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public final static String ARG_TREEREDUCIBLE = "-nt";
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public final static String ARG_NANOSCHEDULABLE = "-nct";
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public final static String CMDLINE_GATK_URL = GATK_DOCS_URL + "org_broadinstitute_sting_gatk_CommandLineGATK.html";
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public final static String CMDLINE_GATK_URL = GATK_DOCS_URL + "org_broadinstitute_gatk_engine_CommandLineGATK.php";
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/**
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* Definition of the group names / categories of tools.
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@ -44,7 +44,7 @@ public class HelpUtils {
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*/
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public static void listAnnotations() {
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System.out.println("\nThis is a list of available Variant Annotations for use with tools such as UnifiedGenotyper, HaplotypeCaller and VariantAnnotator. Please see the Technical Documentation for more details about these annotations:");
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System.out.println("http://www.broadinstitute.org/gatk/gatkdocs/");
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System.out.println("http://www.broadinstitute.org/gatk/tooldocs/");
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System.out.println("\nStandard annotations in the list below are marked with a '*'.");
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List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = new PluginManager<InfoFieldAnnotation>(InfoFieldAnnotation.class).getPlugins();
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System.out.println("\nAvailable annotations for the VCF INFO field:");
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@ -32,65 +32,13 @@
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<#global guideIndex = "http://www.broadinstitute.org/gatk/guide/" />
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<#global forum = "http://gatkforums.broadinstitute.org/" />
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<#macro makeHeader title isIndex>
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<?php ob_start(); ?>
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<!DOCTYPE html>
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<html lang='en'>
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<head>
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<meta charset='utf-8'>
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<title>${title} documentation</title>
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<meta name='viewport' content='width=device-width, initial-scale=1.0'>
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<meta name='description' content=''>
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<link type="text/css" rel="stylesheet" href="bootstrap.min.css">
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<script src="jquery.min.js"></script>
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<script src="bootstrap.min.js"></script>
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<style>
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@media (min-width: 980px) {
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body {
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padding-top : 60px;
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}
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}
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</style>
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<!-- MathJax / MathML support for displaying equations -->
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<script type='text/x-mathjax-config'>
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MathJax.Hub.Config({
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TeX: { equationNumbers: { autoNumber: 'AMS' } }
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});
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</script>
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<script type='text/javascript' src='http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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</head>
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<body>
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<div class="navbar navbar-fixed-top">
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<div class="navbar-inner">
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<div class="container-fluid">
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<a class="brand" href="index.html">GATK | Tool Documentation</a>
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</div>
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</div>
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</div>
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<div class="container-fluid">
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<?php
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// Output Buffering allows for the website to inject a different header
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ob_clean();
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include '../include/common.php';
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printHeader("${title}", "Guides");
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?>
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<div class="row-fluid">
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<#if isIndex>
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<?php printGATKDocsNav(); ?>
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<div class="span9">
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</#if>
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</#macro>
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<#macro footerInfo>
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<hr>
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<p><a href='#top'><i class='fa fa-chevron-up'></i> Return to top</a></p>
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<hr>
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<p class="see-also">See also
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<a href="${guideIndex}">Guide Index</a> |
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<a href="index.html">Tool Documentation Index</a> |
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<a href="index">Tool Documentation Index</a> |
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<a href="${forum}">Support Forum</a>
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</p>
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@ -103,15 +51,6 @@
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</p>
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</#macro>
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<#macro pageFooter>
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</div><!--/.span-->
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</div><!--/.row-->
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</body>
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<?php printFooter();
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ob_end_flush();
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?>
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</#macro>
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<#macro getCategories groups>
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<style>
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#sidenav .accordion-body a {
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@ -22,6 +22,19 @@
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~ OTHER DEALINGS IN THE SOFTWARE.
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-->
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<?php
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include '../../../include/common.php';
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$module = modules::GATK;
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printHeader($module, "GATK | Tool Documentation Index", "Guides");
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?>
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<div class='row-fluid'>
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<?php printGATKDocsNav($module); ?>
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<div class='span9'>
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<#include "common.html"/>
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<#macro emitGroup group>
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@ -53,8 +66,7 @@
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</div>
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</#macro>
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<@makeHeader title="GATK | Tool Documentation Index" isIndex=true />
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<h1>Tool Documentation Index
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<h1 id="top">Tool Documentation Index
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<small>${version}</small>
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</h1>
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<div class="accordion" id="index">
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@ -71,4 +83,11 @@
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<@footerInfo />
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<@footerClose />
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<@pageFooter />
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</div></div>
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<?php
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printFooter($module);
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?>
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@ -22,6 +22,15 @@
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~ OTHER DEALINGS IN THE SOFTWARE.
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-->
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<?php
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include '../../../include/common.php';
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$module = modules::GATK;
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printHeader($module, "GATK | Tool Documentation Index", "Guides");
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?>
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<div class='row-fluid' id="top">
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<#include "common.html"/>
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<#macro argumentlist name myargs>
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@ -113,8 +122,11 @@
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</#macro>
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<?php $group = '${group}'; ?>
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<@makeHeader title="GATK | ${name} documentation" isIndex=false />
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<section class="span4">
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<aside class="well">
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<a href="index"><h4><i class='fa fa-chevron-left'></i> Back to Tool Docs Index</h4></a>
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</aside>
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<aside class="well">
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<h2>Categories</h2>
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<@getCategories groups=groups />
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@ -300,4 +312,7 @@
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<small>GTD: ${gotoDev}</small>
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</#if>
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<@footerClose />
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<@pageFooter />
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</div>
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<?php printFooter($module); ?>
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