Merge pull request #34 from biopet/Fix_BIOPET_557

Changed VCFstats to check whether outputDir is a valid directory.

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala

@@ -74,7 +74,7 @@ object VcfStats extends ToolCommand {
     opt[File]('o', "outputDir") required () unbounded () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(outputDir = x)
     } validate {
-      x => if (x == null) failure("Output directory required") else success
+      x => if (x == null) failure("Valid output directory required") else if (x.exists) success else failure(s"Output directory does not exist: $x")
     } text "Path to directory for output (required)"
     opt[File]('i', "intervals") unbounded () valueName "<file>" action { (x, c) =>
       c.copy(intervals = Some(x))

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala

@@ -15,15 +15,16 @@
 package nl.lumc.sasc.biopet.tools
 
 import java.io.File
-import java.nio.file.{ Files, Paths }
+import java.nio.file.{Files, Paths}
 
 import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.tools.vcfstats.{ SampleStats, SampleToSampleStats, Stats, VcfStats }
+import nl.lumc.sasc.biopet.tools.vcfstats.{SampleStats, SampleToSampleStats, Stats, VcfStats}
 import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats._
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 import nl.lumc.sasc.biopet.utils.sortAnyAny
+import org.apache.commons.io.FileUtils
 
 import scala.collection.mutable
 
@@ -162,6 +163,16 @@ class VcfStatsTest extends TestNGSuite with Matchers {
     valueFromTsv(i, "Sample_ID_3", "bam") should be(empty)
   }
 
+  @Test
+  def testNoExistOutputDir: Unit = {
+    val tmp = Files.createTempDirectory("vcfStats")
+    FileUtils.deleteDirectory(new File(tmp.toAbsolutePath.toString))
+    val vcf = resourcePath("/chrQ.vcf.gz")
+    val ref = resourcePath("/fake_chrQ.fa")
+
+    an [IllegalArgumentException] should be thrownBy main(Array("-I", vcf, "-R", ref, "-o", tmp.toAbsolutePath.toString))
+  }
+
   @Test
   def testMain() = {
     val tmp = Files.createTempDirectory("vcfStats")