Adding basic testing

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala

+package nl.lumc.sasc.biopet.utils.intervals
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 24/08/15.
+ */
+class BedRecordTest extends TestNGSuite with Matchers {
+  @Test def testLineParse: Unit = {
+    BedRecord("chrQ", 0, 4) shouldBe BedRecord("chrQ", 0, 4)
+    BedRecord.fromLine("chrQ\t0\t4") shouldBe BedRecord("chrQ", 0, 4)
+    BedRecord.fromLine("chrQ\t0\t4\tname\t3\t+") shouldBe BedRecord("chrQ", 0, 4, Some("name"), Some(3.0), Some(true))
+    BedRecord.fromLine("chrQ\t0\t4\tname\t3\t+\t1\t3") shouldBe
+      BedRecord("chrQ", 0, 4, Some("name"), Some(3.0), Some(true), Some(1), Some(3))
+    BedRecord.fromLine("chrQ\t0\t4\tname\t3\t+\t1\t3\t255,0,0") shouldBe
+      BedRecord("chrQ", 0, 4, Some("name"), Some(3.0), Some(true), Some(1), Some(3), Some((255,0,0)))
+    BedRecord.fromLine("chrQ\t0\t100\tname\t3\t+\t1\t3\t255,0,0\t2\t10,20\t20,50") shouldBe
+      BedRecord("chrQ", 0, 100, Some("name"), Some(3.0), Some(true), Some(1), Some(3), Some((255,0,0)),
+        Some(2), IndexedSeq(10,20), IndexedSeq(20,50))
+  }
+
+  @Test def testLineOutput: Unit = {
+    BedRecord("chrQ", 0, 4).toString shouldBe "chrQ\t0\t4"
+    BedRecord.fromLine("chrQ\t0\t4").toString shouldBe "chrQ\t0\t4"
+  }
+
+  @Test def testOverlap: Unit = {
+    BedRecord("chrQ", 0, 4).overlapWith(BedRecord("chrQ", 0, 4)) shouldBe true
+    BedRecord("chrQ", 0, 4).overlapWith(BedRecord("chrX", 0, 4)) shouldBe false
+    BedRecord("chrQ", 0, 4).overlapWith(BedRecord("chrQ", 4, 8)) shouldBe false
+    BedRecord("chrQ", 0, 4).overlapWith(BedRecord("chrQ", 3, 8)) shouldBe true
+    BedRecord("chrQ", 4, 8).overlapWith(BedRecord("chrQ", 0, 4)) shouldBe false
+    BedRecord("chrQ", 3, 4).overlapWith(BedRecord("chrQ", 0, 4)) shouldBe true
+    BedRecord("chrQ", 3, 4).overlapWith(BedRecord("chrQ", 4, 5)) shouldBe false
+  }
+
+  @Test def testLength: Unit = {
+    BedRecord("chrQ", 0, 4).length shouldBe 4
+    BedRecord("chrQ", 0, 1).length shouldBe 1
+    BedRecord("chrQ", 3, 4).length shouldBe 1
+    BedRecord.fromLine("chrQ\t0\t100\tname\t3\t+\t1\t3\t255,0,0\t2\t10,20\t20,50").exons.get.foldLeft(0)(_ + _.length) shouldBe 30
+    BedRecord.fromLine("chrQ\t0\t100\tname\t3\t+\t1\t3\t255,0,0\t2\t10,20\t20,50").introns.get.foldLeft(0)(_ + _.length) shouldBe 20
+  }
+
+  @Test def testErrors: Unit = {
+    BedRecord("chrQ", 0, 3).validate
+    BedRecord.fromLine("chrQ\t0\t100\tname\t3\t+\t1\t3\t255,0,0\t2\t10,20\t20,50").validate
+    intercept[IllegalArgumentException] {
+      BedRecord("chrQ", 0, 0).validate
+    }
+    intercept[IllegalArgumentException] {
+      BedRecord("chrQ", 4, 3).validate
+    }
+    intercept[IllegalArgumentException] {
+      BedRecord.fromLine("chrQ\t0\t100\tname\t3\t+\t1\t3\t255,0,0\t2\t10\t50").validate
+    }
+    intercept[IllegalStateException] {
+      BedRecord.fromLine("chrQ\t0\t100\tname\t3\tx\t1\t3\t255,0,0\t2\t10,20\t20,50").validate
+    }
+  }
+}