From a09831489b150424ba78f973028ffbe1e7d20fea Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Tue, 6 Aug 2013 16:45:11 -0400 Subject: [PATCH] Disabled emission of doc URLs for external codecs to avoid broken links --- .../gatk/refdata/tracks/FeatureManager.java | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java index 68e751521..60b6f4683 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java @@ -225,10 +225,20 @@ public class FeatureManager { docs.append(String.format(format, nameHeader, featureHeader, docHeader)); for ( final FeatureDescriptor descriptor : featureDescriptors ) { if ( requiredFeatureType.isAssignableFrom(descriptor.getFeatureClass()) ) { - String oneDoc = String.format(format, - descriptor.getName(), - descriptor.getSimpleFeatureName(), - GATKDocUtils.helpLinksToGATKDocs(descriptor.getCodecClass())); + final String DocURL = GATKDocUtils.helpLinksToGATKDocs(descriptor.getCodecClass()); + final String oneDoc; + if ( DocURL.contains("_sting_") ) { + 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); } }