PrefixFastqTest

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.samtools.fastq.FastqReader
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.collection.JavaConversions._
+
+
+/**
+ * Created by ahbbollen on 28-8-15.
+ */
+class PrefixFastqTest extends TestNGSuite with MockitoSugar with Matchers {
+
+  import PrefixFastq._
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  val fq = resourcePath("/paired01a.fq")
+
+  @Test
+  def testMain() = {
+    val temp = File.createTempFile("out", ".fastq")
+
+    val args = Array("-i", fq, "-o", temp.getAbsolutePath, "-s", "AAA")
+    main(args)
+  }
+
+  @Test
+  def testOutput() = {
+    val temp = File.createTempFile("out", ".fastq")
+
+    val args = Array("-i", fq, "-o", temp.getAbsolutePath, "-s", "AAA")
+    main(args)
+
+    val reader = new FastqReader(temp)
+
+    for (read <- reader.iterator()){
+      read.getReadString.startsWith("AAA") shouldBe true
+    }
+  }
+}