Library fix for Queue/GATK 3.2

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

@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 
 class CalculateHsMetrics(val root:Configurable) extends Picard {
-  javaMainClass = "net.sf.picard.analysis.directed.CalculateHsMetrics"
+  javaMainClass = "picard.analysis.directed.CalculateHsMetrics"
   
   @Input(doc="The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: File = _

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

@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 
 class CollectGcBiasMetrics(val root:Configurable) extends Picard {
-  javaMainClass = "net.sf.picard.analysis.CollectGcBiasMetrics"
+  javaMainClass = "picard.analysis.CollectGcBiasMetrics"
 
   @Input(doc="The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: Seq[File] = Nil

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

@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 
 class CollectInsertSizeMetrics(val root:Configurable) extends Picard {
-  javaMainClass = "net.sf.picard.analysis.CollectInsertSizeMetrics"
+  javaMainClass = "picard.analysis.CollectInsertSizeMetrics"
 
   @Input(doc="The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: File = _

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

@@ -5,8 +5,8 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 
 class MarkDuplicates(val root:Configurable) extends Picard {
-  javaMainClass = "net.sf.picard.sam.MarkDuplicates"
-
+  javaMainClass = "picard.sam.MarkDuplicates"
+  
   @Input(doc="The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: List[File] = Nil