Added unit test

biopet-tools/src/test/resources/paired01_post_filter.fq

+@r01_filter hello
+A
++
+H
+@r03_filter
+G
++
+H

biopet-tools/src/test/resources/paired01_pre_filter.fq

+@r01_filter hello
+A
++
+H
+@r02
+T
++
+I
+@r03_filter
+G
++
+H
+@r04
+C
++
+I
+@r05
+A
++
+H

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

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+ * Created by ahbbollen on 27-8-15.
+ */
+class FastqFilterTest extends TestNGSuite with MockitoSugar with Matchers {
+
+  import FastqFilter._
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  val preFilterFastq = resourcePath("/paired01_pre_filter.fq")
+  val postFilterFastq = resourcePath("/paired01_post_filter.fq")
+
+  @Test
+  def testMain() = {
+    val temp = File.createTempFile("out", ".fastq")
+    temp.deleteOnExit()
+    val args = Array("-I", preFilterFastq, "-o", temp.getAbsolutePath, "--idRegex", "_filter$")
+    main(args)
+
+    Source.fromFile(temp).getLines().toList shouldBe Source.fromFile(postFilterFastq).getLines().toList
+  }
+
+}