Added SeqtkSeq function to Flexiprep

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala

@@ -4,7 +4,7 @@
  * @author  Wibowo Arindrarto
  */
 
-package nl.lumc.sasc.biopet.function.seqtk
+package nl.lumc.sasc.biopet.extensions.seqtk
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala

@@ -4,7 +4,7 @@
  * @author  Wibowo Arindrarto
  */
 
-package nl.lumc.sasc.biopet.function.seqtk
+package nl.lumc.sasc.biopet.extensions.seqtk
 
 import java.io.File
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala

+/*
+ * 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
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.Ln
+
+class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq(root) {
+  var fastqc: Fastqc = _
+
+  override def beforeCmd {
+    super.beforeCmd
+    if (fastqc != null && Q == None) {
+      Q = fastqc.getEncoding match {
+        case null => None
+        case s if (s.contains("Sanger / Illumina 1.9")) => None
+        case s if (s.contains("Illumina <1.3")) => Option(64)
+        case s if (s.contains("Illumina 1.3")) => Option(64)
+        case s if (s.contains("Illumina 1.5")) => Option(64)
+      }
+      if (Q != None) V = true
+    }
+  }
+  
+  override def cmdLine = {
+    if (Q != None) {
+      analysisName = getClass.getName
+      super.cmdLine
+    } else {
+      analysisName = getClass.getSimpleName + "-ln"
+      Ln(this, input, output).cmd
+    }
+  }
+}