Merge branch 'feature-varianteval' into 'develop'

Feature varianteval

for ticket #82 , Queue wrapper around the GATK class..

See merge request !30

biopet-framework/nb-configuration.xml

@@ -25,6 +25,5 @@ Any value defined here will override the pom.xml file value but is only applicab
         <com-junichi11-netbeans-changelf.use-global>false</com-junichi11-netbeans-changelf.use-global>
         <com-junichi11-netbeans-changelf.show-dialog>true</com-junichi11-netbeans-changelf.show-dialog>
         <org-netbeans-modules-javascript2-requirejs.enabled>true</org-netbeans-modules-javascript2-requirejs.enabled>
-        <netbeans.hint.jdkPlatform>JDK_1.8</netbeans.hint.jdkPlatform>
     </properties>
 </project-shared-configuration>

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

+package nl.lumc.sasc.biopet.extensions.gatk
+
+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 afterGraph {
+    super.afterGraph
+  }
+}
+
+object VariantEval {
+  def apply(root: Configurable, sample: File, compareWith: File,
+            output: File): VariantEval = {
+    val vareval = new VariantEval(root)
+    vareval.eval = Seq(sample)
+    vareval.comp = Seq(compareWith)
+    vareval.out = output
+    vareval.afterGraph
+    return vareval
+  }
+
+  def apply(root: Configurable, sample: File, compareWith: File,
+            output: File, ST: Seq[String], EV: Seq[String]): VariantEval = {
+    val vareval = new VariantEval(root)
+    vareval.eval = Seq(sample)
+    vareval.comp = Seq(compareWith)
+    vareval.out = output
+    vareval.noST = true
+    vareval.ST = ST
+    vareval.noEV = true
+    vareval.EV = EV
+    vareval.afterGraph
+    return vareval
+  }
+
+}
\ No newline at end of file

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala

@@ -5,8 +5,8 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.gatk.SelectVariants
+import nl.lumc.sasc.biopet.extensions.gatk.VariantEval
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.queue.extensions.gatk.{ CommandLineGATK, VariantEval }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
 
 class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQScript {
@@ -28,12 +28,6 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
   var sampleVcfs: Map[String, File] = Map()
   def generalSampleDir = outputDir + "samples/"
 
-  trait gatkArguments extends CommandLineGATK {
-    this.reference_sequence = reference
-    this.memoryLimit = 2
-    this.jobResourceRequests :+= "h_vmem=4G"
-  }
-
   def init() {
     if (reference == null) reference = config("reference")
     if (config.contains("target_bed"))
@@ -70,14 +64,13 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
     for ((sample, sampleVcf) <- sampleVcfs) {
       val sampleDir = generalSampleDir + sample + File.separator
       for ((compareSample, compareSampleVcf) <- sampleVcfs) {
-        val variantEval = new VariantEval with gatkArguments
-        variantEval.eval = Seq(sampleVcf)
-        variantEval.comp = Seq(compareSampleVcf)
-        variantEval.out = new File(sampleDir + sample + "-" + compareSample + ".eval.txt")
-        variantEval.noST = true
-        variantEval.ST = Seq("VariantType", "CompRod")
-        variantEval.noEV = true
-        variantEval.EV = Seq("CompOverlap")
+        val variantEval = VariantEval(this,
+          sampleVcf,
+          compareSampleVcf,
+          new File(sampleDir + sample + "-" + compareSample + ".eval.txt"),
+          Seq("VariantType", "CompRod"),
+          Seq("CompOverlap")
+        )
         if (targetBed != null) variantEval.L = targetBed
         add(variantEval)
         sampleCompareMetrics.deps ::= variantEval.out