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Disabled emission of doc URLs for external codecs to avoid broken links

This commit is contained in:
Geraldine Van der Auwera 2013-08-06 16:45:11 -04:00
parent 4d20c71e09
commit a09831489b
1 changed files with 14 additions and 4 deletions
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18
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
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@ -225,10 +225,20 @@ public class FeatureManager {
docs.append(String.format(format, nameHeader, featureHeader, docHeader)); docs.append(String.format(format, nameHeader, featureHeader, docHeader));
for ( final FeatureDescriptor descriptor : featureDescriptors ) { for ( final FeatureDescriptor descriptor : featureDescriptors ) {
if ( requiredFeatureType.isAssignableFrom(descriptor.getFeatureClass()) ) { if ( requiredFeatureType.isAssignableFrom(descriptor.getFeatureClass()) ) {
String oneDoc = String.format(format, final String DocURL = GATKDocUtils.helpLinksToGATKDocs(descriptor.getCodecClass());
descriptor.getName(), final String oneDoc;
descriptor.getSimpleFeatureName(), if ( DocURL.contains("_sting_") ) {
GATKDocUtils.helpLinksToGATKDocs(descriptor.getCodecClass())); oneDoc = String.format(format,
descriptor.getName(),
descriptor.getSimpleFeatureName(),
DocURL);
} else {
oneDoc = String.format(format,
descriptor.getName(),
descriptor.getSimpleFeatureName(),
"(this is an external codec and is not documented within GATK)");
}
docs.append(oneDoc); docs.append(oneDoc);
} }
} }