Commit 4dcbb9cd authored by Sander Bollen's avatar Sander Bollen
Browse files

proper temp files

parent b4bb3fd3
......@@ -45,19 +45,25 @@ class CheckAllelesVcfInBamTest extends TestNGSuite with MockitoSugar with Matche
val rand = new Random()
@Test def testOutputTypeVcf() = {
val tmp_path = "/tmp/CheckAllesVcfInBam_" + rand.nextString(10) + ".vcf"
val tmp = File.createTempFile("CheckAllelesVcfInBam", ".vcf")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments = Array("-I", vcf, "-b", bam, "-s", "sample01", "-o", tmp_path)
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
val tmp_path = "/tmp/CheckAllesVcfInBam_" + rand.nextString(10) + ".vcf.gz"
val tmp = File.createTempFile("CheckAllelesVcfInBam", ".vcf.gz")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments = Array("-I", vcf, "-b", bam, "-s", "sample01", "-o", tmp_path)
main(arguments)
}
@Test def testOutputTypeBcf() = {
val tmp_path = "/tmp/CheckAllesVcfInBam_" + rand.nextString(10) + ".bcf"
val tmp = File.createTempFile("CheckAllelesVcfInBam", ".bcf")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments = Array("-I", vcf, "-b", bam, "-s", "sample01", "-o", tmp_path)
main(arguments)
}
......
......@@ -15,6 +15,7 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.File
import java.nio.file.Paths
import org.scalatest.Matchers
......@@ -48,19 +49,25 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
val rand = new Random()
@Test def testOutputTypeVcf() = {
val tmp_path = "/tmp/MergeAlleles_" + rand.nextString(10) + ".vcf"
val tmp = File.createTempFile("MergeAlleles", ".vcf")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments = Array("-I", vepped_path, "-o", tmp_path, "-R", reference)
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
val tmp_path = "/tmp/MergeAlleles_" + rand.nextString(10) + ".vcf.gz"
val tmp = File.createTempFile("MergeAlleles", ".vcf.gz")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments = Array("-I", vepped_path, "-o", tmp_path, "-R", reference)
main(arguments)
}
@Test def testOutputTypeBcf() = {
val tmp_path = "/tmp/MergeAlleles_" + rand.nextString(10) + ".bcf"
val tmp = File.createTempFile("MergeAlleles", ".bcf")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments = Array("-I", vepped_path, "-o", tmp_path, "-R", reference)
main(arguments)
}
......
......@@ -44,19 +44,25 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
val rand = new Random()
@Test def testOutputTypeVcf() = {
val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf"
val tmp = File.createTempFile("VcfFilter", ".vcf")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
main(arguments)
}
@Test def testOutputTypeBcf() = {
val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".bcf"
val tmp = File.createTempFile("VcfFilter", ".bcf")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf.gz"
val tmp = File.createTempFile("VcfFilter", ".vcf.gz")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
main(arguments)
}
......
......@@ -15,6 +15,7 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.File
import java.nio.file.Paths
import org.scalatest.Matchers
......@@ -41,19 +42,25 @@ class VcfToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
val unvepped = resourcePath("/unvepped.vcf")
@Test def testAllFields() = {
val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
val tmp = File.createTempFile("VcfToTsv", ".tsv")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments = Array("-I", unvepped, "-o", tmp_path, "--all_info")
main(arguments)
}
@Test def testSpecificField() = {
val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
val tmp = File.createTempFile("VcfToTsv", ".tsv")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments = Array("-I", vepped, "-o", tmp_path, "-i", "CSQ")
main(arguments)
}
@Test def testNewSeparators() = {
val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
val tmp = File.createTempFile("VcfToTsv", ".tsv")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
val arguments = Array("-I", vepped, "-o", tmp_path, "--all_info", "--separator", ",", "--list_separator", "|")
main(arguments)
}
......
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