Add tool to replace python script

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

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommand
+import htsjdk.samtools.fastq.{ FastqRecord, AsyncFastqWriter, FastqReader, BasicFastqWriter }
+import scala.collection.JavaConversions._
+
+/**
+ * Created by pjvan_thof on 1/13/15.
+ */
+object PrefixFastq extends ToolCommand {
+  case class Args(input: File = null, output: File = null, seq: String = "CATG") extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('i', "input") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
+      c.copy(input = x)
+    }
+    opt[File]('o', "output") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
+      c.copy(output = x)
+    }
+    opt[String]('s', "seq") maxOccurs (1) valueName ("<prefix seq>") action { (x, c) =>
+      c.copy(seq = x)
+    }
+  }
+
+  /**
+   * @param args the command line arguments
+   */
+  def main(args: Array[String]): Unit = {
+    logger.info("Start")
+
+    val argsParser = new OptParser
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+    val writer = new AsyncFastqWriter(new BasicFastqWriter(cmdArgs.output), 3000)
+    val reader = new FastqReader(cmdArgs.input)
+
+    var counter = 0
+    while (reader.hasNext) {
+      val read = reader.next()
+
+      val maxQuality = read.getBaseQualityString.max
+
+      val readHeader = read.getReadHeader
+      val readSeq = cmdArgs.seq + read.getReadString
+      val baseQualityHeader = read.getBaseQualityHeader
+      val baseQuality = Array.fill(cmdArgs.seq.size)(maxQuality).mkString + read.getBaseQualityString
+
+      writer.write(new FastqRecord(readHeader, readSeq, baseQualityHeader, baseQuality))
+
+      counter += 1
+      if (counter % 1e6 == 0) logger.info(counter + " reads processed")
+    }
+
+    if (counter % 1e6 != 0) logger.info(counter + " reads processed")
+    writer.close()
+    reader.close()
+    logger.info("Done")
+  }
+}