Commit 3c33ec7e authored by Sander Bollen's avatar Sander Bollen
Browse files

PrefixFastqTest

parent 6638216b
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
}
}
}
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