Use TestNGSuite and Matchers in WipeReads test

biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/apps/WipeReadsUnitTest.scala

@@ -9,13 +9,12 @@ import java.io.{ File, IOException }
 import scala.collection.JavaConverters._
 
 import htsjdk.samtools._
-import org.scalatest.Assertions
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
-/* TODO: helper function to create SAMRecord from SAM alignment string
-         so we can test as if using real SAMRecords
-*/
-class WipeReadsUnitTest extends Assertions {
+
+class WipeReadsUnitTest extends TestNGSuite with Matchers {
 
   import WipeReads._
 
@@ -103,13 +102,13 @@ class WipeReadsUnitTest extends Assertions {
 
   @Test def testMakeRawIntervalFromBED() = {
     val intervals: Vector[RawInterval] = makeRawIntervalFromFile(BEDFile1).toVector
-    assert(intervals.length == 3)
-    assert(intervals.last.chrom == "chrQ")
-    assert(intervals.last.start == 291)
-    assert(intervals.last.end == 320)
-    assert(intervals.head.chrom == "chrQ")
-    assert(intervals.head.start == 991)
-    assert(intervals.head.end == 1000)
+    intervals.length should be (3)
+    intervals.head.chrom should === ("chrQ")
+    intervals.head.start should be (991)
+    intervals.head.end should be (1000)
+    intervals.last.chrom should === ("chrQ")
+    intervals.last.start should be (291)
+    intervals.last.end should be (320)
   }
 
   @Test def testSingleBAMDefault() = {
@@ -368,9 +367,9 @@ class WipeReadsUnitTest extends Assertions {
     val exp = new SAMFileReader(sBAMFile3).asScala
     val obs = new SAMFileReader(outBAM).asScala
     for ((e, o) <- exp.zip(obs))
-      assert(e.getSAMString === o.getSAMString)
-    assert(outBAM.exists)
-    assert(outBAMIndex.exists)
+      e.getSAMString should === (o.getSAMString)
+    outBAM should be ('exists)
+    outBAMIndex should be ('exists)
   }
 
   @Test def testWriteSingleBAMAndFilteredBAM() = {
@@ -387,11 +386,11 @@ class WipeReadsUnitTest extends Assertions {
     val exp = new SAMFileReader(sBAMFile4).asScala
     val obs = new SAMFileReader(filteredOutBAM).asScala
     for ((e, o) <- exp.zip(obs))
-      assert(e.getSAMString === o.getSAMString)
-    assert(outBAM.exists)
-    assert(outBAMIndex.exists)
-    assert(filteredOutBAM.exists)
-    assert(filteredOutBAMIndex.exists)
+      e.getSAMString should === (o.getSAMString)
+    outBAM should be ('exists)
+    outBAMIndex should be ('exists)
+    filteredOutBAM should be ('exists)
+    filteredOutBAMIndex should be ('exists)
   }
 
   @Test def testWritePairBAMDefault() = {
@@ -404,8 +403,8 @@ class WipeReadsUnitTest extends Assertions {
     val exp = new SAMFileReader(pBAMFile3).asScala
     val obs = new SAMFileReader(outBAM).asScala
     for ((e, o) <- exp.zip(obs))
-      assert(e.getSAMString === o.getSAMString)
-    assert(outBAM.exists)
-    assert(outBAMIndex.exists)
+      e.getSAMString should === (o.getSAMString)
+    outBAM should be ('exists)
+    outBAMIndex should be ('exists)
   }
 }
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