Commit 0065cfb1 authored by Sander Bollen's avatar Sander Bollen

add test for numberRoutput

parent daa546d8
......@@ -73,7 +73,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test
def testOutputFieldException = {
def testOutputFieldException() = {
val tmpFile = File.createTempFile("VCFWithVCf", ".vcf")
tmpFile.deleteOnExit()
val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:AC", "-R", referenceFasta)
......@@ -83,7 +83,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test
def testInputFieldException = {
def testInputFieldException() = {
val tmpFile = File.createTempFile("VCFWithVCf", ".vcf")
tmpFile.deleteOnExit()
val args = Array("-I", unveppedPath, "-s", unveppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:NEW_CSQ", "-R", referenceFasta)
......@@ -93,7 +93,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test
def testMinMethodException = {
def testMinMethodException() = {
val tmpFile = File.createTempFile("VcfWithVcf_", ".vcf")
tmpFile.deleteOnExit()
val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:CSQ:min", "-R", referenceFasta)
......@@ -103,7 +103,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test
def testMaxMethodException = {
def testMaxMethodException() = {
val tmpFile = File.createTempFile("VcfWithVcf_", ".vcf")
tmpFile.deleteOnExit()
val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:CSQ:max", "-R", referenceFasta)
......@@ -113,7 +113,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test
def testFieldMap = {
def testFieldMap() = {
val unvepReader = new VCFFileReader(new File(unveppedPath))
val header = unvepReader.getFileHeader
val unvepRecord = unvepReader.iterator().next()
......@@ -174,7 +174,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test
def testGetSecondaryRecords = {
def testGetSecondaryRecords() = {
val unvepRecord = new VCFFileReader(new File(unveppedPath)).iterator().next()
val vepReader = new VCFFileReader(new File(veppedPath))
val vepRecord = vepReader.iterator().next()
......@@ -185,7 +185,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test
def testCreateRecord = {
def testCreateRecord() = {
val unvepRecord = new VCFFileReader(new File(unveppedPath)).iterator().next()
val vepReader = new VCFFileReader(new File(veppedPath))
val header = vepReader.getFileHeader
......@@ -218,7 +218,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test
def testNumberAOutput = {
def testNumberAOutput() = {
val tmpFile = File.createTempFile("numberA", ".vcf.gz")
tmpFile.deleteOnExit()
val arguments = Array("-I", monoPath, "-s", multiPath, "-o", tmpFile.getAbsolutePath, "-f", "AF:MULTI_AF", "-R", referenceFasta)
......@@ -228,4 +228,18 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test
def testNumberROutput() = {
val tmpFile = File.createTempFile("numberR", ".vcf.gz")
tmpFile.deleteOnExit()
val arguments = Array("-I", monoPath, "-s", multiPath, "-o", tmpFile.getAbsolutePath, "-f", "ALL_ALLELE:MULTI_ALL_ALLELE", "-R", referenceFasta)
main(arguments)
val annotatedRecord = new VCFFileReader(tmpFile).iterator().next()
annotatedRecord.getAttribute("MULTI_ALL_ALLELE") match {
case l: List[_] => l shouldBe List("C", "A")
case u: util.ArrayList[_] => u.toList shouldBe List("C", "A")
case _ => throw new IllegalStateException("Not a list")
}
}
}
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