Commit b4583a4d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added Reference to gentrap test

parent a6e3dbc8
@HD VN:1.4 SO:unsorted
@SQ SN:chr1 LN:9 UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa M5:fe15dbbd0900310caf32827f6da57550
......@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.gentrap
import java.io.File
import java.io.{ FileOutputStream, File }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.AggrBaseCount
......@@ -186,8 +186,20 @@ class GentrapTest extends TestNGSuite with Matchers {
object GentrapTest {
val outputDir = Files.createTempDir()
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
val os = new FileOutputStream(new File(outputDir, name))
org.apache.commons.io.IOUtils.copy(is, os)
os.close()
}
copyFile("ref.fa")
copyFile("ref.dict")
copyFile("ref.fa.fai")
val executables = Map(
"reference" -> "test",
"reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"dict" -> "test",
"annotation_gtf" -> "test",
"annotation_bed" -> "test",
......
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