Add automatic sample detection

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

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 import java.io.PrintWriter
+import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import nl.lumc.sasc.biopet.core.ToolCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
@@ -59,6 +60,16 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
     val samtoolsMpileup = new SamtoolsMpileup(this)
   }
 
+  override def beforeCmd: Unit = {
+    if (sample == null && inputBam.exists()) {
+      val inputSam = SamReaderFactory.makeDefault.open(inputBam)
+      val readGroups = inputSam.getFileHeader.getReadGroups
+      val samples = readGroups.map(readGroup => readGroup.getSample).distinct
+      sample = samples.head
+      inputSam.close
+    }
+  }
+
   override def commandLine = {
     (if (inputMpileup == null) {
       val samtoolsMpileup = new SamtoolsMpileup(this)