diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd index 2b8d6db9f..dc7a08287 100644 --- a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd +++ b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd @@ -19,9 +19,9 @@ Medical and Population Genetics Program Maintainer: Kiran Garimella } \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{ ## get script arguments in interactive and non-interactive mode diff --git a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java index 976889613..15ec9dfe5 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java +++ b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java @@ -287,8 +287,8 @@ public abstract class CommandLineProgram { * a function used to indicate an error occurred in the command line tool */ private static void printDocumentationReference() { - errorPrintf("Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki%n"); - errorPrintf("Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa%n"); + errorPrintf("Visit our website and forum for extensive documentation and answers to %n"); + errorPrintf("commonly asked questions http://www.broadinstitute.org/gatk%n"); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index c0865e656..d8674c606 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -35,9 +35,10 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.gatk.walkers.Attribution; 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.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 java.util.*; @@ -142,8 +143,7 @@ public class CommandLineGATK extends CommandLineExecutable { List header = new ArrayList(); 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("Please view our documentation at http://www.broadinstitute.org/gsa/wiki"); - header.add("For support, please view our support site at http://getsatisfaction.com/gsa"); + header.add("For support and documentation go to http://www.broadinstitute.org/gatk"); return header; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java index ef0909c2f..21db1412b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.indels; +import net.sf.samtools.*; import org.apache.commons.jexl2.Expression; import org.apache.commons.jexl2.JexlContext; import org.apache.commons.jexl2.JexlEngine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java index cdf7b19c6..1b5474777 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval; +import com.google.java.contract.Requires; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.util.IntervalTree; import net.sf.samtools.SAMSequenceRecord; diff --git a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala index 7a22e700b..041e84a8c 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala @@ -205,8 +205,7 @@ class QCommandLine extends CommandLineProgram with Logging { private def createQueueHeader() : Seq[String] = { Seq(String.format("Queue v%s, Compiled %s", getQueueVersion, getBuildTimestamp), "Copyright (c) 2012 The Broad Institute", - "Please view our documentation at http://www.broadinstitute.org/gsa/wiki", - "For support, please view our support site at http://getsatisfaction.com/gsa") + "Fro support and documentation go to http://www.broadinstitute.org/gatk") } private def getQueueVersion : String = {