Commit 723cb3e4 authored by Sander Bollen's avatar Sander Bollen
Browse files

AnnotateVcfWithBedTest stub and improve argument descriptions in AnnotateVcfWithBed

parent 31d6ba36
......@@ -56,10 +56,10 @@ object AnnotateVcfWithBed extends ToolCommand {
class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required () unbounded () valueName ("<vcf file>") action { (x, c) =>
c.copy(inputFile = x)
} text ("out is a required file property")
} text ("Input is a required file property")
opt[File]('B', "bedFile") required () unbounded () valueName ("<bed file>") action { (x, c) =>
c.copy(bedFile = x)
} text ("out is a required file property")
} text ("Bedfile is a required file property")
opt[File]('o', "output") required () unbounded () valueName ("<vcf file>") action { (x, c) =>
c.copy(outputFile = x)
} text ("out is a required file property")
......
package nl.lumc.sasc.biopet.tools
import java.nio.file.Paths
import org.testng.annotations.Test
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import scala.util.Random
/**
* Created by ahbbollen on 9-4-15.
*/
class AnnotateVcfWithBedTest extends TestNGSuite with MockitoSugar with Matchers {
import AnnotateVcfWithBed._
private def resourcePath(p: String): String = {
Paths.get(getClass.getResource(p).toURI).toString
}
val vepped_path = resourcePath("/VEP_oneline.vcf")
val bed = resourcePath("/rrna01.bed")
val rand = new Random()
@Test def testOutputTypeVcf() = {
val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf"
val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path, "-B", bed, "-f", "testing")
main(arguments)
}
@Test def testOutputTypeBcf() = {
val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".bcf"
val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path, "-B", bed, "-f", "testing")
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf.gz"
val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path, "-B", bed, "-f", "testing")
main(arguments)
}
}
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