Update to Queue/GATK 3.2

.gitignore

@@ -4,4 +4,6 @@
 /pipeline-template/nbactions.xml
 /gatk-variantcalling/nbactions.xml
 /gatk-variantcalling/dependency-reduced-pom.xml
-/bam-metrics/nbactions.xml
\ No newline at end of file
+/bam-metrics/nbactions.xml
+dependency-reduced-pom.xml
+nbactions.xml

bam-metrics/pom.xml

@@ -55,7 +55,7 @@
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>queue-package</artifactId>
-            <version>3.1</version>
+            <version>3.2</version>
         </dependency>
     </dependencies>
     <build>

bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

 package nl.lumc.sasc.biopet.pipelines.bammetrics
 
 import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
-import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.gatk.queue.QScript
 import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
 import java.io.File
 import nl.lumc.sasc.biopet.core.apps.{BedToInterval, BiopetFlagstat}

bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics.scripts
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 
 class CoverageStats(val root:Configurable) extends PythonCommandLineFunction {

biopet-framework/pom.xml

@@ -52,7 +52,7 @@
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>queue-package</artifactId>
-            <version>3.1</version>
+            <version>3.2</version>
         </dependency>
     </dependencies>
     <build>

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

 package nl.lumc.sasc.biopet.core
 
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline._
 import scala.sys.process._
 import nl.lumc.sasc.biopet.core.config._
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

@@ -2,9 +2,9 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.queue.QException
-import org.broadinstitute.sting.queue.function.CommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.queue.QException
+import org.broadinstitute.gatk.queue.function.CommandLineFunction
+import org.broadinstitute.gatk.utils.commandline._
 import scala.sys.process._
 import scala.util.matching.Regex
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

 package nl.lumc.sasc.biopet.core
 
-import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
+import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
 
 abstract class BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
   executeble = "java"

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala

@@ -27,21 +27,21 @@
 package nl.lumc.sasc.biopet.core
 
 import java.io.File
-import org.broadinstitute.sting.commandline._
-import org.broadinstitute.sting.queue.util._
-import org.broadinstitute.sting.queue.QCommandPlugin
-import org.broadinstitute.sting.queue.QScript
-import org.broadinstitute.sting.queue.QScriptManager
-import org.broadinstitute.sting.queue.engine.{QStatusMessenger, QGraphSettings, QGraph}
+import org.broadinstitute.gatk.utils.commandline._
+import org.broadinstitute.gatk.queue.util._
+import org.broadinstitute.gatk.queue.QCommandPlugin
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.QScriptManager
+import org.broadinstitute.gatk.queue.engine.{QStatusMessenger, QGraphSettings, QGraph}
 import collection.JavaConversions._
-import org.broadinstitute.sting.utils.classloader.PluginManager
-import org.broadinstitute.sting.utils.exceptions.UserException
-import org.broadinstitute.sting.utils.io.IOUtils
-import org.broadinstitute.sting.utils.help.ApplicationDetails
+import org.broadinstitute.gatk.utils.classloader.PluginManager
+import org.broadinstitute.gatk.utils.exceptions.UserException
+import org.broadinstitute.gatk.utils.io.IOUtils
+import org.broadinstitute.gatk.utils.help.ApplicationDetails
 import java.io.FileOutputStream
 import java.net.URL
 import java.util.{ResourceBundle, Arrays}
-import org.broadinstitute.sting.utils.text.TextFormattingUtils
+import org.broadinstitute.gatk.utils.text.TextFormattingUtils
 import org.apache.commons.io.FilenameUtils
 
 /**

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -3,9 +3,9 @@ package nl.lumc.sasc.biopet.core
 import java.io.File
 import java.io.PrintWriter
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.commandline._
-import org.broadinstitute.sting.queue.QSettings
-import org.broadinstitute.sting.queue.function.QFunction
+import org.broadinstitute.gatk.utils.commandline._
+import org.broadinstitute.gatk.queue.QSettings
+import org.broadinstitute.gatk.queue.function.QFunction
 
 trait BiopetQScript extends Configurable {
   @Argument(doc="Config Json file",shortName="config", required=false)

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.FileOutputStream
 //import org.broadinstitute.sting.queue.QCommandLine
-import org.broadinstitute.sting.queue.util.Logging
+import org.broadinstitute.gatk.queue.util.Logging
 
 trait PipelineCommand extends Logging {
 //  val src = ""

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BedToInterval.scala

 package nl.lumc.sasc.biopet.core.apps
 
+import htsjdk.samtools.SAMFileReader
+import htsjdk.samtools.SAMSequenceRecord
 import java.io.File
-import net.sf.samtools.SAMSequenceRecord
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 import java.io.PrintWriter
-import net.sf.samtools.SAMFileReader
 import scala.io.Source
 
 class BedToInterval(val root:Configurable) extends BiopetJavaCommandLineFunction {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BiopetFlagstat.scala

 package nl.lumc.sasc.biopet.core.apps
 
+import htsjdk.samtools.SAMFileReader
+import htsjdk.samtools.SAMRecord
 import java.io.{BufferedInputStream, File, FileInputStream, PrintWriter}
-import net.sf.samtools.SAMFileReader
-import net.sf.samtools.SAMRecord
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import scala.io.Source
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Input, Output}
-import org.broadinstitute.sting.queue.util.Logging
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.queue.util.Logging
 import scala.collection.JavaConversions._
 import scala.collection.mutable.Map
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/FastqSplitter.scala

@@ -5,7 +5,7 @@ import java.util.zip.GZIPInputStream
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import scala.io.Source
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
 class FastqSplitter(val root:Configurable) extends BiopetJavaCommandLineFunction {
   javaMainClass = getClass.getName

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core.config
 import nl.lumc.sasc.biopet.core._
 import scala.util.parsing.json._
 import java.io.File
-import org.broadinstitute.sting.queue.util.Logging
+import org.broadinstitute.gatk.queue.util.Logging
 
 class Config(var map: Map[String,Any]) extends Logging {
   logger.debug("Init phase of config")

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

 package nl.lumc.sasc.biopet.core.config
 
 import java.io.File
-import org.broadinstitute.sting.queue.util.Logging
+import org.broadinstitute.gatk.queue.util.Logging
 
 trait Configurable extends Logging {
   val root: Configurable

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline._
 import java.io.File
 
 class Cat(val root:Configurable) extends BiopetCommandLineFunction {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala

@@ -2,8 +2,8 @@ package nl.lumc.sasc.biopet.function
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.queue.function.InProcessFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.queue.function.InProcessFunction
+import org.broadinstitute.gatk.utils.commandline._
 import java.io.File
 import scala.sys.process._
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.function
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 //import org.broadinstitute.sting.queue.function.CommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline._
 import java.io.File
 
 class Pbzip2(val root:Configurable) extends BiopetCommandLineFunction {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
 
 import java.io.FileOutputStream
 import nl.lumc.sasc.biopet.core._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline._
 import java.io.File
 import scala.collection.JavaConversions._