Fix reference

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala

@@ -17,20 +17,20 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
  * Created by pjvan_thof on 3/3/15.
  */
-class Freebayes(val root: Configurable) extends BiopetCommandLineFunction {
+class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with Reference {
 
   @Input(required = true)
   var bamfiles: List[File] = Nil
 
   @Input(required = true)
-  var reference: File = config("reference")
+  var reference: File = _
 
   @Output(required = true)
   var outputVcf: File = null
@@ -42,6 +42,11 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction {
   override val versionRegex = """version:  (.*)""".r
   override def versionCommand = executable + " --version"
 
+  override def beforeGraph: Unit = {
+    super.beforeGraph
+    reference = referenceFasta()
+  }
+
   def cmdLine = executable +
     required("--fasta-reference", reference) +
     repeat("--bam", bamfiles) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala

@@ -15,12 +15,13 @@
  */
 package nl.lumc.sasc.biopet.extensions.samtools
 
+import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
 /** Extension for samtools mpileup */
-class SamtoolsMpileup(val root: Configurable) extends Samtools {
+class SamtoolsMpileup(val root: Configurable) extends Samtools with Reference {
   @Input(doc = "Bam File")
   var input: List[File] = Nil
 
@@ -28,7 +29,7 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
   var output: File = _
 
   @Input(doc = "Reference fasta")
-  var reference: File = config("reference")
+  var reference: File = _
 
   @Input(doc = "Interval bed", required = false)
   var intervalBed: Option[File] = config("interval_bed")
@@ -40,6 +41,11 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
   var depth: Option[Int] = config("depth")
   var outputMappingQuality: Boolean = config("output_mapping_quality", default = false)
 
+  override def beforeGraph: Unit = {
+    super.beforeGraph
+    reference = referenceFasta()
+  }
+
   def cmdBase = required(executable) +
     required("mpileup") +
     optional("-f", reference) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 import java.io.PrintWriter
 import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
 import nl.lumc.sasc.biopet.utils.ConfigUtils
@@ -29,7 +29,7 @@ import scala.math.round
 import scala.math.floor
 import scala.collection.JavaConversions._
 
-class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion {
+class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Reference {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input mpileup file", shortName = "mpileup", required = false)
@@ -46,7 +46,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion {
   var homoFraction: Option[Double] = config("homoFraction")
   var ploidy: Option[Int] = config("ploidy")
   var sample: String = _
-  var reference: String = config("reference")
+  var reference: String = _
 
   override val defaultCoreMemory = 3.0
 
@@ -55,6 +55,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion {
 
   override def beforeGraph {
     super.beforeGraph
+    reference = referenceFasta().getAbsolutePath
     val samtoolsMpileup = new SamtoolsMpileup(this)
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala

@@ -21,7 +21,7 @@ import htsjdk.samtools.reference.FastaSequenceFile
 import htsjdk.variant.variantcontext.{ Allele, VariantContext, Genotype }
 import htsjdk.variant.vcf.VCFFileReader
 import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
-import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 import scala.collection.JavaConversions._
@@ -35,7 +35,7 @@ import scala.util.Random
 /**
  * Created by pjvan_thof on 1/10/15.
  */
-class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summarizable {
+class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summarizable with Reference {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input fastq", shortName = "I", required = true)
@@ -59,9 +59,10 @@ class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summariza
   var genotypeTags: List[String] = Nil
   var allInfoTags = false
   var allGenotypeTags = false
-  var reference: File = config("reference")
+  var reference: File = _
 
   override def beforeGraph: Unit = {
+    reference = referenceFasta()
     index = new File(input.getAbsolutePath + ".tbi")
   }