diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java index 4966817de..3aa402220 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java @@ -42,7 +42,6 @@ public class VCFStreamingIntegrationTest extends WalkerTest { public void testSimpleVCFStreaming() throws IOException { // Create a FIFO. This seems to be the only way to create an interprocess FIFO in Java (java.nio.Pipe is intraprocess only). File tmpFifo = File.createTempFile("vcfstreaming",""); - tmpFifo.deleteOnExit(); Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()}); @@ -55,24 +54,24 @@ public class VCFStreamingIntegrationTest extends WalkerTest { inputStream.close(); WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants" + - " -R " + b36KGReference + - " -B:variant,vcf " + tmpFifo.getAbsolutePath() + - " -rit STREAM --NO_HEADER" + - " -o %s", + "-T SelectVariants " + + "-R " + b36KGReference + " " + + "-B:variant,vcf " + tmpFifo.getAbsolutePath() + " " + + "-rit STREAM --NO_HEADER " + + "-o %s", 1, Arrays.asList("2cae3d16f9ed00b07d87e9c49272d877") ); executeTest("testSimpleVCFStreaming", spec); + tmpFifo.delete(); } @Test public void testVCFStreamingChain() throws IOException { // Create a FIFO. This seems to be the only way to create an interprocess FIFO in Java (java.nio.Pipe is intraprocess only). File tmpFifo = File.createTempFile("vcfstreaming",""); - tmpFifo.deleteOnExit(); Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()}); String testFile = validationDataLocation + "yri.trio.gatk.ug.head.vcf"; @@ -104,5 +103,6 @@ public class VCFStreamingIntegrationTest extends WalkerTest { ); executeTest("testVCFStreamingChain", selectTestSpec); + tmpFifo.delete(); } }