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GATK Error messages now point to the new website instead of GetSatisfaction.

This commit is contained in:
Mauricio Carneiro 2012-07-20 17:16:24 -04:00
parent 116885a450
commit d446d34227
6 changed files with 11 additions and 10 deletions
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4
public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd
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@ -19,9 +19,9 @@ Medical and Population Genetics Program
Maintainer: Kiran Garimella Maintainer: Kiran Garimella
} }
\references{ \references{
GSA wiki page: http://www.broadinstitute.org/gsa/wiki GSA wiki page: http://www.broadinstitute.org/gatk
GATK help forum: http://www.getsatisfaction.com/gsa GATK help forum: http://www.broadinstitute.org/gatk
} }
\examples{ \examples{
## get script arguments in interactive and non-interactive mode ## get script arguments in interactive and non-interactive mode

4
public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
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@ -287,8 +287,8 @@ public abstract class CommandLineProgram {
* a function used to indicate an error occurred in the command line tool * a function used to indicate an error occurred in the command line tool
*/ */
private static void printDocumentationReference() { private static void printDocumentationReference() {
errorPrintf("Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki%n"); errorPrintf("Visit our website and forum for extensive documentation and answers to %n");
errorPrintf("Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa%n"); errorPrintf("commonly asked questions http://www.broadinstitute.org/gatk%n");
} }

8
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -35,9 +35,10 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.gatk.walkers.Attribution; import org.broadinstitute.sting.gatk.walkers.Attribution;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.*; 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.text.TextFormattingUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.util.*; import java.util.*;
@ -142,8 +143,7 @@ public class CommandLineGATK extends CommandLineExecutable {
List<String> header = new ArrayList<String>(); List<String> header = new ArrayList<String>();
header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime())); 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("Copyright (c) 2010 The Broad Institute");
header.add("Please view our documentation at http://www.broadinstitute.org/gsa/wiki"); header.add("For support and documentation go to http://www.broadinstitute.org/gatk");
header.add("For support, please view our support site at http://getsatisfaction.com/gsa");
return header; return header;
} }

1
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.indels; package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.*;
import org.apache.commons.jexl2.Expression; import org.apache.commons.jexl2.Expression;
import org.apache.commons.jexl2.JexlContext; import org.apache.commons.jexl2.JexlContext;
import org.apache.commons.jexl2.JexlEngine; import org.apache.commons.jexl2.JexlEngine;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.varianteval; package org.broadinstitute.sting.gatk.walkers.varianteval;
import com.google.java.contract.Requires;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.util.IntervalTree; import net.sf.picard.util.IntervalTree;
import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMSequenceRecord;

3
public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
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@ -205,8 +205,7 @@ class QCommandLine extends CommandLineProgram with Logging {
private def createQueueHeader() : Seq[String] = { private def createQueueHeader() : Seq[String] = {
Seq(String.format("Queue v%s, Compiled %s", getQueueVersion, getBuildTimestamp), Seq(String.format("Queue v%s, Compiled %s", getQueueVersion, getBuildTimestamp),
"Copyright (c) 2012 The Broad Institute", "Copyright (c) 2012 The Broad Institute",
"Please view our documentation at http://www.broadinstitute.org/gsa/wiki", "Fro support and documentation go to http://www.broadinstitute.org/gatk")
"For support, please view our support site at http://getsatisfaction.com/gsa")
} }
private def getQueueVersion : String = { private def getQueueVersion : String = {