Added find overlap tool

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

+package nl.lumc.sasc.biopet.tools
+
+import java.io.{File, PrintWriter}
+
+import nl.lumc.sasc.biopet.utils.ToolCommand
+
+import scala.collection.mutable.ListBuffer
+import scala.io.Source
+
+/**
+ * Created by pjvan_thof on 21-9-16.
+ */
+object FindOverlapMatch extends ToolCommand {
+
+  case class Args(inputVcf: File = null,
+                  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)
+    }
+    opt[Double]('c', "cutoff") required () unbounded () valueName "<value>" action { (x, c) =>
+      c.copy(cutoff = x)
+    }
+  }
+
+  /**
+   * @param args the command line arguments
+   */
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val cmdargs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
+
+    val reader = Source.fromFile(cmdargs.inputVcf)
+
+    val data = reader.getLines().map(_.split("\t")).toArray
+
+    val samples = data.head.zipWithIndex.tail
+
+    var overlap = 0
+    var multiOverlap = 0
+    var noOverlap = 0
+
+    for (i1 <- samples) {
+      val buffer = ListBuffer[(String, Double)]()
+      for (i2 <- samples ) {
+        val value = data(i1._2)(i2._2).toDouble
+        if (value >= cmdargs.cutoff && i1._2 != i2._2) {
+          buffer.+=((i2._1, value))
+        }
+      }
+      if (buffer.nonEmpty) overlap += 1
+      else noOverlap += 1
+      if (buffer.size > 1) multiOverlap += 1
+
+      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")
+  }
+}