FindRepeatsPacBioTest

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

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.samtools.{SamReaderFactory, QueryInterval}
+import nl.lumc.sasc.biopet.tools.FastqSplitter._
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.collection.immutable.Nil
+
+/**
+ * Created by ahbbollen on 27-8-15.
+ */
+class FindRepeatsPacBioTest extends TestNGSuite with MockitoSugar with Matchers {
+
+  import FindRepeatsPacBio._
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  val bed = resourcePath("/rrna01.bed")
+  val bam = resourcePath("/paired01.bam")
+
+  @Test
+  def testMain() = {
+
+    val args = Array("-I", bam, "-b", bed)
+    main(args)
+  }
+
+  @Test
+  def testResult() = {
+    val samReader = SamReaderFactory.makeDefault().open(new File(bam))
+    val header = samReader.getFileHeader
+    val record = samReader.iterator().next()
+    val interval = new QueryInterval(header.getSequenceIndex("chrQ"), 50, 55)
+    val result = procesSamrecord(record, interval)
+
+    result.isEmpty shouldBe false
+
+    result.get.samRecord shouldEqual record
+    result.get.beginDel should be >= 0
+    result.get.endDel should be >= 0
+  }
+
+  @Test
+  def testResultObject = {
+    val record = SamReaderFactory.makeDefault().open(new File(bam)).iterator().next()
+    val result = new Result
+    result.samRecord = record
+
+    result.samRecord shouldEqual record
+    result.beginDel shouldBe 0
+    result.endDel shouldBe 0
+    result.dels shouldEqual Nil
+    result.ins shouldEqual Nil
+  }
+
+
+}