Merged bug fix from Stable into Unstable

public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java

@@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
 import org.broadinstitute.sting.utils.help.HelpFormatter;
+import org.broadinstitute.sting.utils.help.HelpUtils;
 
 import java.io.IOException;
 import java.util.*;
@@ -288,7 +289,7 @@ public abstract class CommandLineProgram {
      */
     private static void printDocumentationReference() {
         errorPrintf("Visit our website and forum for extensive documentation and answers to %n");
-        errorPrintf("commonly asked questions http://www.broadinstitute.org/gatk%n");
+        errorPrintf("commonly asked questions " + HelpUtils.BASE_GATK_URL + "%n");
     }
 
 

public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.help.GATKDocUtils;
+import org.broadinstitute.sting.utils.help.HelpUtils;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
 import java.util.*;
@@ -160,7 +161,7 @@ public class CommandLineGATK extends CommandLineExecutable {
         List<String> header = new ArrayList<String>();
         header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime()));
         header.add("Copyright (c) 2010 The Broad Institute");
-        header.add("For support and documentation go to http://www.broadinstitute.org/gatk");
+        header.add("For support and documentation go to " + HelpUtils.BASE_GATK_URL);
         return header;
     }
 

public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java

@@ -25,11 +25,9 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import com.google.common.base.Function;
-import com.google.common.collect.Collections2;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.help.GATKDocUtils;
+import org.broadinstitute.sting.utils.help.HelpUtils;
 
 import java.util.Collection;
 import java.util.List;
@@ -73,7 +71,7 @@ public class FilterManager extends PluginManager<ReadFilter> {
 
         return String.format("Read filter %s not found. Available read filters:%n%n%s%n%n%s",pluginName,
                 userFriendlyListofReadFilters(availableFilters),
-                "Please consult the GATK Documentation (http://www.broadinstitute.org/gatk/gatkdocs/) for more information.");
+                "Please consult the GATK Documentation (" + HelpUtils.GATK_DOCS_URL + ") for more information.");
     }
 
     private String userFriendlyListofReadFilters(List<Class<? extends ReadFilter>> filters) {

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java

@@ -282,7 +282,8 @@ public class DiffEngine {
         // now that we have a specific list of values we want to show, display them
         GATKReport report = new GATKReport();
         final String tableName = "differences";
-        report.addTable(tableName, "Summarized differences between the master and test files. See http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information", 3);
+        // TODO for Geraldine -- link needs to be updated below
+        report.addTable(tableName, "Summarized differences between the master and test files. See [ask Geraldine to fix link to DiffEngine wiki] for more information", 3);
         final GATKReportTable table = report.getTable(tableName);
         table.addColumn("Difference");
         table.addColumn("NumberOfOccurrences");

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java

@@ -138,6 +138,7 @@ public class DiffObjects extends RodWalker<Integer, Integer> {
     /**
      * Writes out a file of the DiffEngine format:
      *
+     *     TODO for Geraldine -- link needs to be updated below (and also in SelectVariants and RefSeqCodec GATK docs)
      *     http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
      */
     @Output(doc="File to which results should be written",required=true)

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java

@@ -13,7 +13,7 @@ import java.util.Set;
 /**
  * Stratifies the eval RODs by user-supplied JEXL expressions
  *
- * See http://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions for more details
+ * See http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk for more details
  */
 public class JexlExpression extends VariantStratifier implements StandardStratification {
     // needs to know the jexl expressions

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

@@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.help.HelpUtils;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -80,7 +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 http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator");
+                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");
             }
 
             foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java

@@ -51,8 +51,7 @@ import java.util.*;
  * The Variant Validation Assessor is a tool for vetting/assessing validation data (containing genotypes).
  * The tool produces a VCF that is annotated with information pertaining to plate quality control and by
  * default is soft-filtered by high no-call rate or low Hardy-Weinberg probability.
- * If you have .ped files, please first convert them to VCF format
+ * If you have .ped files, please first convert them to VCF format.
- * (see http://www.broadinstitute.org/gsa/wiki/index.php/Converting_ped_to_vcf).
  *
  * <h2>Input</h2>
  * <p>

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

@@ -30,6 +30,7 @@ import net.sf.samtools.SAMSequenceDictionary;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.sting.utils.help.HelpUtils;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
@@ -267,7 +268,7 @@ 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 http://www.broadinstitute.org/gsa/wiki/index.php/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.GATK_FORUM_URL + "discussion/59/companion-utilities-replacereadgroups to fix this problem", read.getReadName()));
         }
     }
 
@@ -343,7 +344,7 @@ 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: http://www.broadinstitute.org/gsa/wiki/index.php/ReorderSam"
+                    + "\nYou can use the ReorderSam utility to fix this problem: " + HelpUtils.GATK_FORUM_URL + "discussion/58/companion-utilities-reordersam"
                     + "\n  %s contigs = %s",
                     name, name, ReadUtils.prettyPrintSequenceRecords(dict)));
         }

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

@@ -44,14 +44,13 @@ public class ForumAPIUtils {
     /**
      * How we post to the forum
      */
-    private final static String API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
     final private static String ACCESS_TOKEN = "access_token=";
 
     public static List<String> getPostedTools(String forumKey) {
         Gson gson = new Gson();
         List<String> output = new ArrayList<String>();
 
-        String text = httpGet(API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
+        String text = httpGet(HelpUtils.GATK_FORUM_API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
 
         APIQuery details = gson.fromJson(text, APIQuery.class);
         ForumDiscussion[] discussions = details.Discussions;
@@ -159,7 +158,7 @@ public class ForumAPIUtils {
         Gson gson = new Gson();
 
         String data = gson.toJson(post.getPostData());
-        httpPost(data, API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
+        httpPost(data, HelpUtils.GATK_FORUM_API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
 
 
     }
@@ -167,8 +166,7 @@ public class ForumAPIUtils {
     class APIQuery {
         ForumDiscussion[] Discussions;
 
-        public APIQuery() {
+        public APIQuery() {}
-        }
     }
 
 }

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

@@ -28,7 +28,7 @@ public class GATKDocUtils {
     /**
      * The URL root for RELEASED GATKDOC units
      */
-    public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gatk/gatkdocs/";
+    public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpUtils.GATK_DOCS_URL;
     /**
      * The URL root for STABLE GATKDOC units
      */

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

@@ -32,6 +32,15 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import java.lang.reflect.Field;
 
 public class HelpUtils {
+
+    public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk";
+    public final static String GATK_DOCS_URL = BASE_GATK_URL + "/gatkdocs/";
+    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/";
+
+
+
+
     protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
         try {
             Class type = getClassForDoc(classDoc);

public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java

@@ -71,7 +71,6 @@ abstract class SortingVariantContextWriterBase implements VariantContextWriter {
         this.takeOwnershipOfInner = takeOwnershipOfInner;
 
         // has to be PriorityBlockingQueue to be thread-safe
-        // see http://getsatisfaction.com/gsa/topics/missing_loci_output_in_multi_thread_mode_when_implement_sortingvcfwriterbase?utm_content=topic_link&utm_medium=email&utm_source=new_topic
         this.queue = new PriorityBlockingQueue<VCFRecord>(50, new VariantContextComparator());
 
         this.mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC;

public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java

@@ -28,7 +28,6 @@ public class VCFIntegrationTest extends WalkerTest {
     }
 
     @Test(enabled = true)
-    // See https://getsatisfaction.com/gsa/topics/support_vcf_4_1_structural_variation_breakend_alleles?utm_content=topic_link&utm_medium=email&utm_source=new_topic
     public void testReadingAndWritingBreakpointAlleles() {
         String testVCF = privateTestDir + "breakpoint-example.vcf";