Merge branch 'fix-warns' into 'develop'

Fix warns

Going to try to fix most of the code warnings from the IDE
Also going to optimise imports for the whole repository

See merge request !187

protected/biopet-gatk-extensions/pom.xml

@@ -9,7 +9,6 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 
-    <groupId>nl.lumc.sasc</groupId>
     <artifactId>BiopetGatkExtensions</artifactId>
     <packaging>jar</packaging>
     

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class AnalyzeCovariates(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.AnalyzeCovariates with GatkGeneral {
@@ -17,6 +18,6 @@ object AnalyzeCovariates {
     ac.before = before
     ac.after = after
     ac.plots = plots
-    return ac
+    ac
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

@@ -6,13 +6,14 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
   scatterCount = config("scattercount", default = 0)
 
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
 
     nt = Option(getThreads(3))
     memoryLimit = Option(nt.getOrElse(1) * 2)
@@ -36,6 +37,6 @@ object ApplyRecalibration {
     ar.recal_file = recal_file
     ar.tranches_file = tranches_file
     ar.out = output
-    return ar
+    ar
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.BaseRecalibrator with GatkGeneral {
@@ -19,7 +20,7 @@ object BaseRecalibrator {
     val br = new BaseRecalibrator(root)
     br.input_file :+= input
     br.out = output
-    br.beforeGraph
-    return br
+    br.beforeGraph()
+    br
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class CombineGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineGVCFs with GatkGeneral {
@@ -17,6 +18,6 @@ object CombineGVCFs {
     val cg = new CombineGVCFs(root)
     cg.variant = input
     cg.o = output
-    return cg
+    cg
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class CombineVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineVariants with GatkGeneral {
@@ -17,6 +18,6 @@ object CombineVariants {
     val cv = new CombineVariants(root)
     cv.variant = input
     cv.out = output
-    return cv
+    cv
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -5,7 +5,7 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
+import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 
 trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction with Reference {
@@ -27,10 +27,10 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
   override def versionExitcode = List(0, 1)
   override def versionCommand = executable + " -jar " + jarFile + " -version"
 
-  override def getVersion = super.getVersion.collect { case version => "Gatk " + version }
+  override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
 
-  override def beforeGraph: Unit = {
-    super.beforeGraph
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
     if (reference_sequence == null) reference_sequence = referenceFasta()
   }
 }

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.GenotypeGVCFs with GatkGeneral {
@@ -28,6 +29,6 @@ object GenotypeGVCFs {
     val gg = new GenotypeGVCFs(root)
     gg.variant = gvcfFiles
     gg.out = output
-    return gg
+    gg
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

@@ -35,8 +35,8 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
     stand_emit_conf = config("stand_emit_conf", default = 0)
   }
 
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
     if (bamOutput != null && nct.getOrElse(1) > 1) {
       threads = 1
       logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
@@ -18,6 +19,6 @@ object IndelRealigner {
     ir.input_file :+= input
     ir.targetIntervals = targetIntervals
     ir.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bam")
-    return ir
+    ir
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {
@@ -17,6 +18,6 @@ object PrintReads {
     val br = new PrintReads(root)
     br.input_file :+= input
     br.out = output
-    return br
+    br
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {
@@ -19,6 +20,6 @@ object RealignerTargetCreator {
     val re = new RealignerTargetCreator(root)
     re.input_file :+= input
     re.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.intervals")
-    return re
+    re
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class SelectVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.SelectVariants with GatkGeneral {
@@ -17,6 +18,6 @@ object SelectVariants {
     val sv = new SelectVariants(root)
     sv.variant = input
     sv.out = output
-    return sv
+    sv
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

@@ -26,8 +26,8 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
     }
   }
 
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
 
     genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
     nct = Some(getThreads(1))

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class VariantAnnotator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantAnnotator with GatkGeneral {
@@ -19,6 +20,6 @@ object VariantAnnotator {
     va.variant = input
     va.input_file = bamFiles
     va.out = output
-    return va
+    va
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

@@ -6,11 +6,12 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
   }
 }
 
@@ -21,8 +22,8 @@ object VariantEval {
     vareval.eval = Seq(sample)
     vareval.comp = Seq(compareWith)
     vareval.out = output
-    vareval.beforeGraph
-    return vareval
+    vareval.beforeGraph()
+    vareval
   }
 
   def apply(root: Configurable, sample: File, compareWith: File,
@@ -35,8 +36,8 @@ object VariantEval {
     vareval.ST = ST
     vareval.noEV = true
     vareval.EV = EV
-    vareval.beforeGraph
-    return vareval
+    vareval.beforeGraph()
+    vareval
   }
 
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
 
@@ -38,6 +39,6 @@ object VariantRecalibrator {
     vr.input :+= input
     vr.recal_file = recal_file
     vr.tranches_file = tranches_file
-    return vr
+    vr
   }
 }
\ No newline at end of file

protected/biopet-gatk-pipelines/pom.xml

@@ -9,7 +9,6 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 
-    <groupId>nl.lumc.sasc</groupId>
     <artifactId>BiopetGatkPipelines</artifactId>
     <packaging>jar</packaging>
     

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala

@@ -11,6 +11,8 @@ import nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
 import org.broadinstitute.gatk.queue.QScript
 
 /**
+ * Basty pipeline including GATK steps
+ *
  * Created by pjvan_thof on 3/4/15.
  */
 class Basty(val root: Configurable) extends QScript with BastyTrait {

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

@@ -5,10 +5,10 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+
 import scala.util.Random
 
 class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with BiopetQScript {
@@ -38,7 +38,7 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
     var gvcfPool: List[File] = Nil
     addGenotypingPipeline(gvcfPool)
 
-    while (todoGvcfs.size > 0) {
+    while (todoGvcfs.nonEmpty) {
       val index = Random.nextInt(todoGvcfs.size)
       gvcfPool ::= todoGvcfs(index)
       addGenotypingPipeline(gvcfPool)
@@ -51,8 +51,8 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
     gatkGenotyping.inputGvcfs = sampleGvcf :: gvcfPool
     gatkGenotyping.samples :+= sampleName
     gatkGenotyping.outputDir = new File(outputDir, "samples_" + gvcfPool.size)
-    gatkGenotyping.init
-    gatkGenotyping.biopetScript
+    gatkGenotyping.init()
+    gatkGenotyping.biopetScript()
     addAll(gatkGenotyping.functions)
   }
 }