Added unit testing

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

@@ -8,13 +8,16 @@ import scala.collection.mutable.ListBuffer
 import scala.io.Source
 
 /**
+ * This tool will find all pairs above a cutoff in a data table
+ *
  * Created by pjvan_thof on 21-9-16.
  */
 object FindOverlapMatch extends ToolCommand {
 
   case class Args(inputMetrics: File = null,
                   outputFile: Option[File] = None,
-                  cutoff: Double = 0.0) extends AbstractArgs
+                  cutoff: Double = 0.0,
+                  filterSameNames: Boolean = true) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
     opt[File]('i', "input") required () unbounded () valueName "<file>" action { (x, c) =>
@@ -26,6 +29,10 @@ object FindOverlapMatch extends ToolCommand {
     opt[Double]('c', "cutoff") required () unbounded () valueName "<value>" action { (x, c) =>
       c.copy(cutoff = x)
     } text "minimum value to report it as pair"
+    opt[Unit]("use_same_names") unbounded () valueName "<value>" action { (x, c) =>
+      c.copy(filterSameNames = false)
+    } text "Do not compare samples with the same name"
+
   }
 
   /**
@@ -55,7 +62,7 @@ object FindOverlapMatch extends ToolCommand {
       val buffer = ListBuffer[(String, Double)]()
       for (i2 <- samplesRowHeader) {
         val value = data(i1._2)(i2._2).toDouble
-        if (value >= cmdArgs.cutoff && i1._2 != i2._2) {
+        if (value >= cmdArgs.cutoff && (!cmdArgs.filterSameNames || i1._2 != i2._2)) {
           buffer.+=((i2._1, value))
         }
       }

biopet-tools/src/test/resources/overlapmetrics.txt

+	sample1	sample2	sample3
+sample1	1.0	0.5	0.9
+sample2	0.5	1.0	0.5
+sample3	0.9	0.5	1.0

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatchTest.scala

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+  * Created by pjvan_thof on 27-9-16.
+  */
+class FindOverlapMatchTest extends TestNGSuite with Matchers {
+
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  @Test
+  def testOverlap: Unit = {
+    val input = new File(resourcePath("/overlapmetrics.txt"))
+    val output = File.createTempFile("overlap.", ".txt")
+    val shouldBeOutput = new File(resourcePath("/overlapmetrics.default.output"))
+    output.deleteOnExit()
+    FindOverlapMatch.main(Array("-i", input.getAbsolutePath, "-c", "0.9", "-o", output.getAbsolutePath))
+    Source.fromFile(output).getLines().toList shouldBe Source.fromFile(shouldBeOutput).getLines().toList
+  }
+
+  @Test
+  def testOverlapSameName: Unit = {
+    val input = new File(resourcePath("/overlapmetrics.txt"))
+    val output = File.createTempFile("overlap.", ".txt")
+    val shouldBeOutput = new File(resourcePath("/overlapmetrics.same_names.output"))
+    output.deleteOnExit()
+    FindOverlapMatch.main(Array("-i", input.getAbsolutePath, "-c", "0.9", "-o", output.getAbsolutePath, "--use_same_names"))
+    Source.fromFile(output).getLines().toList shouldBe Source.fromFile(shouldBeOutput).getLines().toList
+  }
+
+}