Commit b6fac4e1 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Removing comments and stale file

parent 306e857d
/**
* Copyright (c) 2015 Leiden University Medical Center - Sequencing Analysis Support Core <sasc@lumc.nl>
* @author Wai Yi Leung <w.y.leung@lumc.nl>
*/
package nl.lumc.sasc.biopet.tools
import java.io.File
import java.nio.file.Paths
import htsjdk.samtools.fastq.{ FastqReader, FastqRecord }
import nl.lumc.sasc.biopet.core.config.Configurable
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 scala.collection.JavaConverters._
class SeqstatSolexaTest extends TestNGSuite with MockitoSugar with Matchers {
import nl.lumc.sasc.biopet.tools.Seqstat._
private def resourceFile(p: String): File =
new File(resourcePath(p))
private def resourcePath(p: String): String =
Paths.get(getClass.getResource(p).toURI).toString
// Helper functions to create iterator over FastqRecords given its IDs as Ints
private def solexaRecordsOver(ids: String*): java.util.Iterator[FastqRecord] = ids
.map(x => new FastqRecord(x, "ACTGNACTGN", "", "abcd@ABCD@"))
.toIterator.asJava
@DataProvider(name = "mockReaderProvider")
def mockReaderProvider() =
Array(
Array(mock[FastqReader])
)
@Test def testArgsMinimum() = {
val args = Array(
"-i", resourcePath("/paired01a.fq"))
val parsed = parseArgs(args)
parsed.fastq shouldBe resourceFile("/paired01a.fq")
}
}
\ No newline at end of file
......@@ -57,8 +57,6 @@ class SeqstatTest extends TestNGSuite with MockitoSugar with Matchers {
def testEncodingDetectionSanger(fqMock: FastqReader) = {
val seqstat = Seqstat
// val numReads = seqstat.seqStat(fqMock)
// numReads shouldBe 1
seqstat.summarize()
seqstat.phredEncoding shouldBe Sanger
......
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