introduce a level of indirection for the forum URLs - this new function will allow me a place to morph the URL into something that is supported by Confluence

Signed-off-by: Eric Banks <ebanks@broadinstitute.org>

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java

@@ -81,7 +81,7 @@ public class VariantDataManager {
             final double theSTD = standardDeviation(theMean, iii);
             logger.info( annotationKeys.get(iii) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
             if( Double.isNaN(theMean) ) {
-                throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See " + HelpUtils.GATK_FORUM_URL + "discussion/49/using-variant-annotator");
+                throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See " + HelpUtils.forumPost("discussion/49/using-variant-annotator"));
             }
 
             foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);

public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java

@@ -278,7 +278,7 @@ public class UserException extends ReviewedStingException {
 
     public static class ReadMissingReadGroup extends MalformedBAM {
         public ReadMissingReadGroup(SAMRecord read) {
-            super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK.  Please use " + HelpUtils.GATK_FORUM_URL + "discussion/59/companion-utilities-replacereadgroups to fix this problem", read.getReadName()));
+            super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK.  Please use " + HelpUtils.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName()));
         }
     }
 
@@ -354,7 +354,7 @@ public class UserException extends ReviewedStingException {
             super(String.format("Lexicographically sorted human genome sequence detected in %s."
                     + "\nFor safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs."
                     + "\nThis is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files."
-                    + "\nYou can use the ReorderSam utility to fix this problem: " + HelpUtils.GATK_FORUM_URL + "discussion/58/companion-utilities-reordersam"
+                    + "\nYou can use the ReorderSam utility to fix this problem: " + HelpUtils.forumPost("discussion/58/companion-utilities-reordersam")
                     + "\n  %s contigs = %s",
                     name, name, ReadUtils.prettyPrintSequenceRecords(dict)));
         }

public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java

@@ -38,8 +38,9 @@ public class HelpUtils {
     public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/";
     public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
 
-
+    public static String forumPost(String post) {
-
+    	return GATK_FORUM_URL + post;
+    }
 
     protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
         try {