Added getFoundAdapters method

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala

@@ -13,11 +13,6 @@
  * license; For commercial users or users who do not want to follow the AGPL
  * license, please contact us to obtain a separate license.
  */
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
@@ -52,6 +47,30 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
     return null // Could be default Sanger with a warning in the log
   }
 
+  protected case class Sequence(name: String, seq: String)
+  def getFoundAdapters: List[Sequence] = {
+    def getSeqs(file: File) = {
+      if (file != null) {
+        (for (
+          line <- Source.fromFile(file).getLines() if line.startsWith("#");
+          values = line.split("\t") if values.size >= 2
+        ) yield Sequence(values(0), values(1))).toList
+      } else Nil
+    }
+
+    val seqs = getSeqs(adapters) ::: getSeqs(contaminants)
+
+    val block = getDataBlock("Overrepresented sequences")
+    if (block == null) return Nil
+
+    val found = for (
+      line <- block if !line.startsWith("#");
+      values = line.split("\t") if values.size >= 4
+    ) yield values(3)
+
+    seqs.filter(x => found.exists(_.startsWith(x.name)))
+  }
+
   def getSummary: Json = {
     val subfixs = Map("plot_duplication_levels" -> "Images/duplication_levels.png",
       "plot_kmer_profiles" -> "Images/kmer_profiles.png",