Commit 03d1f4f9 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Adding tests for seqstat

parent 8ec0e2da
......@@ -18,12 +18,12 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import java.nio.file.Paths
import htsjdk.samtools.fastq.{ FastqReader, FastqRecord }
import org.mockito.Mockito.{ inOrder => inOrd, when }
import htsjdk.samtools.fastq.{FastqReader, FastqRecord}
import org.mockito.Mockito.{inOrder => inOrd, when}
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{ DataProvider, Test }
import org.testng.annotations.{DataProvider, Test}
import scala.collection.JavaConverters._
......@@ -109,6 +109,23 @@ class SeqStatTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test(dataProvider = "mockReaderProvider", groups = Array("check_readstats"), singleThreaded = true, dependsOnGroups = Array("report"))
def testReadStatsObject(fqMock: FastqReader) = {
when(fqMock.getFile) thenReturn new File("/tmp/test.fq")
when(fqMock.iterator) thenReturn recordsOver("1", "2", "3", "4", "5")
val seqstat = SeqStat
// the histogram should store the lenght==0 value also, for example sequence length 5 is size 6.
// please note that we already loaded the dataset twice in seqstat. (seqstat.Seqstat is called 2 times in previous steps)
seqstat.readStats.lengths(5) shouldBe 10
seqstat.readStats.lengths.length shouldBe 6
seqstat.readStats.nucs.sum shouldBe 50
seqstat.readStats.withN shouldBe 10
}
@Test def testArgsMinimum() = {
val args = Array(
"-i", resourcePath("/paired01a.fq"))
......
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