Commit 7ed7593c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added unit test to SnptestToVcf

parent dca18c6a
# Completed successfully at 2016-04-08 13:47:05
# Analysis: "snptest"
# started: 2016-04-08 13:44:20
#
# Analysis properties:
# -analysis_name snptest (user-supplied)
# -data /exports/sasc/project-171/analysis/snptest/18/18-22307785-33461676.vcf.gz /exports/sasc/project-171/src/Phenotypes_knee_hip_hand.fixed2.txt (user-supplied)
# -o /exports/sasc/project-171/analysis/snptest/18/18-22307785-33461676.snptest (user-supplied)
# -summary_stats_only (user-supplied)
#
alternate_ids rsid chromosome position alleleA alleleB index average_maximum_posterior_call info cohort_1_AA cohort_1_AB cohort_1_BB cohort_1_NULL all_AA all_AB all_BB all_NULL all_total all_maf missing_data_proportion comment
rs184556815 rs184556815 18 22307810 G T 1 1 1 2869 0 0 0 2869 0 0 0 2869 0 0 NA
rs143248971 rs143248971 18 22307875 C T 2 1 1 2869 0 0 0 2869 0 0 0 2869 0 0 NA
rs74666159 rs74666159 18 22307884 C T 3 1 1 2690 177 2 0 2690 177 2 0 2869 0.0315441 0 NA
# Completed successfully at 2016-04-08 13:47:05
......@@ -45,6 +45,4 @@ object GensToVcfTest {
private def resourcePath(p: String): String = {
Paths.get(getClass.getResource(p).toURI).toString
}
}
package nl.lumc.sasc.biopet.tools
import java.io.File
import java.nio.file.Paths
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
/**
* Created by pjvan_thof on 4/11/16.
*/
class SnptestToVcfTest extends TestNGSuite with Matchers {
@Test
def testSnptest: Unit = {
val output = File.createTempFile("test.", ".vcf.gz")
output.deleteOnExit()
SnptestToVcf.main(Array(
"--inputInfo", SnptestToVcfTest.resourcePath("/test.snptest"),
"--outputVcf", output.getAbsolutePath,
"--referenceFasta", SnptestToVcfTest.resourcePath("/fake_chrQ.fa"),
"--contig", "chrQ"
))
}
@Test
def testEmptySnptest: Unit = {
val output = File.createTempFile("test.", ".vcf.gz")
output.deleteOnExit()
SnptestToVcf.main(Array(
"--inputInfo", SnptestToVcfTest.resourcePath("/test.empty.snptest"),
"--outputVcf", output.getAbsolutePath,
"--referenceFasta", SnptestToVcfTest.resourcePath("/fake_chrQ.fa"),
"--contig", "chrQ"
))
}
}
object SnptestToVcfTest {
private def resourcePath(p: String): String = {
Paths.get(getClass.getResource(p).toURI).toString
}
}
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment