Example Scala reading FastQ

fastq_reader.scala

import net.sf.picard.fastq.FastqReader
import java.io.File
import scala.collection.JavaConversions._

object Reader extends App {
  val file = new File(args(0))
  val fr = new FastqReader(file)
  printToFile(new File(args(1)))(p => {
    for (seq <- fr.iterator()) {
      val header = seq.getReadHeader.split(" ")
      if ((header.takeRight(2)(0)) != "/") {
        p.println(">"+header(0)+"/"+header(1)(0)+"\n"+seq.getReadString)
      }
    }
  })

import scala.collection.JavaConversions.asScalaIterator
val reader = new FastqReader(new java.io.File(forward))
for(read <- reader){
println(read.getReadHeader())
}