Added regex option

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

@@ -6,6 +6,7 @@ import nl.lumc.sasc.biopet.utils.ToolCommand
 
 import scala.collection.mutable.ListBuffer
 import scala.io.Source
+import scala.util.matching.Regex
 
 /**
  * This tool will find all pairs above a cutoff in a data table
@@ -17,7 +18,9 @@ object FindOverlapMatch extends ToolCommand {
   case class Args(inputMetrics: File = null,
                   outputFile: Option[File] = None,
                   cutoff: Double = 0.0,
-                  filterSameNames: Boolean = true) extends AbstractArgs
+                  filterSameNames: Boolean = true,
+                  rowSampleRegex: Option[Regex] = None,
+                  columnSampleRegex: Option[Regex] = None) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
     opt[File]('i', "input") required () unbounded () valueName "<file>" action { (x, c) =>
@@ -32,7 +35,12 @@ object FindOverlapMatch extends ToolCommand {
     opt[Unit]("use_same_names") unbounded () valueName "<value>" action { (x, c) =>
       c.copy(filterSameNames = false)
     } text "Do not compare samples with the same name"
-
+    opt[String]("rowSampleRegex") unbounded () valueName "<regex>" action { (x, c) =>
+      c.copy(rowSampleRegex = Some(x.r))
+    }
+    opt[String]("columnSampleRegex") unbounded () valueName "<regex>" action { (x, c) =>
+      c.copy(columnSampleRegex = Some(x.r))
+    }
   }
 
   /**
@@ -58,9 +66,9 @@ object FindOverlapMatch extends ToolCommand {
       case _          => sys.process.stdout
     }
 
-    for (i1 <- samplesColumnHeader) {
+    for (i1 <- samplesColumnHeader if cmdArgs.columnSampleRegex.map(_.findFirstIn(i1._1).isDefined).getOrElse(true)) {
       val buffer = ListBuffer[(String, Double)]()
-      for (i2 <- samplesRowHeader) {
+      for (i2 <- samplesRowHeader if cmdArgs.rowSampleRegex.map(_.findFirstIn(i2._1).isDefined).getOrElse(true)) {
         val value = data(i1._2)(i2._2).toDouble
         if (value >= cmdArgs.cutoff && (!cmdArgs.filterSameNames || i1._2 != i2._2)) {
           buffer.+=((i2._1, value))