Added output file

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala

 package nl.lumc.sasc.biopet.tools
 
-import java.io.File
+import java.io.{File, PrintStream, PrintWriter}
 
 import nl.lumc.sasc.biopet.utils.ToolCommand
 
@@ -12,16 +12,20 @@ import scala.io.Source
  */
 object FindOverlapMatch extends ToolCommand {
 
-  case class Args(inputVcf: File = null,
+  case class Args(inputMetrics: File = null,
+                  outputFile: Option[File] = None,
                   cutoff: Double = 0.0) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
     opt[File]('i', "input") required () unbounded () valueName "<file>" action { (x, c) =>
-      c.copy(inputVcf = x)
-    }
+      c.copy(inputMetrics = x)
+    } text "Input should be a table where the first row and column have the ID's, those can be different"
+    opt[File]('o', "output") unbounded () valueName "<file>" action { (x, c) =>
+      c.copy(outputFile = Some(x))
+    } text "default to stdout"
     opt[Double]('c', "cutoff") required () unbounded () valueName "<value>" action { (x, c) =>
       c.copy(cutoff = x)
-    }
+    } text "minimum value to report it as pair"
   }
 
   /**
@@ -29,23 +33,29 @@ object FindOverlapMatch extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val cmdargs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
-    val reader = Source.fromFile(cmdargs.inputVcf)
+    val reader = Source.fromFile(cmdArgs.inputMetrics)
 
     val data = reader.getLines().map(_.split("\t")).toArray
 
-    val samples = data.head.zipWithIndex.tail
+    val samplesColumnHeader = data.head.zipWithIndex.tail
+    val samplesRowHeader = data.map(_.head).zipWithIndex.tail
 
     var overlap = 0
     var multiOverlap = 0
     var noOverlap = 0
 
-    for (i1 <- samples) {
+    val writer = cmdArgs.outputFile match {
+      case Some(file) => new PrintStream(file)
+      case _ => sys.process.stdout
+    }
+
+    for (i1 <- samplesColumnHeader) {
       val buffer = ListBuffer[(String, Double)]()
-      for (i2 <- samples) {
+      for (i2 <- samplesRowHeader) {
         val value = data(i1._2)(i2._2).toDouble
-        if (value >= cmdargs.cutoff && i1._2 != i2._2) {
+        if (value >= cmdArgs.cutoff && i1._2 != i2._2) {
           buffer.+=((i2._1, value))
         }
       }
@@ -53,10 +63,11 @@ object FindOverlapMatch extends ToolCommand {
       else noOverlap += 1
       if (buffer.size > 1) multiOverlap += 1
 
-      println(s"${i1._1}\t${buffer.mkString("\t")}")
+      writer.println(s"${i1._1}\t${buffer.mkString("\t")}")
     }
     logger.info(s"$overlap found")
     logger.info(s"no $noOverlap found")
     logger.info(s"multi $multiOverlap found")
+    writer.close()
   }
 }