get sample names from vcf when pipeline is started by itself

public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala

@@ -15,10 +15,11 @@
  */
 package nl.lumc.sasc.biopet.utils
 
+import java.io.File
 import java.util
 
 import htsjdk.variant.variantcontext.VariantContext
-import htsjdk.variant.vcf.{ VCFHeader, VCFFilterHeaderLine }
+import htsjdk.variant.vcf.{VCFFileReader, VCFHeader, VCFFilterHeaderLine}
 
 import scala.collection.JavaConversions._
 
@@ -90,4 +91,16 @@ object VcfUtils {
   def isBlockGVcf(header: VCFHeader): Boolean = {
     header.getMetaDataLine("GVCFBlock") != null
   }
+
+  /**
+   * Get sample IDs from vcf File
+   * @param vcf File object pointing to vcf
+   * @return list of strings with sample IDs
+   */
+  def getSampleIds(vcf: File): List[String] = {
+    val reader = new VCFFileReader(vcf, false)
+    val samples = reader.getFileHeader.getSampleNamesInOrder.toList
+    reader.close()
+    samples
+  }
 }

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.extensions.{ Ln, Gzip, VariantEffectPredictor }
 import nl.lumc.sasc.biopet.extensions.tools.{ GvcfToBed, VcfFilter, VcfWithVcf, VepNormalizer }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{VcfUtils, ConfigUtils}
 import org.broadinstitute.gatk.queue.QScript
 
 /**
@@ -43,7 +43,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
     inputFiles :+= new InputFile(inputVCF)
     sampleIds = root match {
       case m: MultiSampleQScript => m.samples.keys.toList
-      case null                  => Nil //TODO: get names from vcf header
+      case null                  => VcfUtils.getSampleIds(inputVCF)
       case s: SampleLibraryTag   => s.sampleId.toList
       case _                     => throw new IllegalArgumentException("You don't have any samples")
     }