zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Some refactoring and cleanup around the area of my sleep-deprived integration 

test typo, which Khalid already fixed for me.  Sorry, Khalid!


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5035 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-01-20 15:03:14 +00:00
parent 3022f4dfa0
commit 8831ec3dce
1 changed files with 7 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
View File

@ -42,7 +42,6 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
public void testSimpleVCFStreaming() throws IOException { 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). // 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",""); File tmpFifo = File.createTempFile("vcfstreaming","");
tmpFifo.deleteOnExit();
Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()}); Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()});
@ -55,24 +54,24 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
inputStream.close(); inputStream.close();
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants" + "-T SelectVariants " +
" -R " + b36KGReference + "-R " + b36KGReference + " " +
" -B:variant,vcf " + tmpFifo.getAbsolutePath() + "-B:variant,vcf " + tmpFifo.getAbsolutePath() + " " +
" -rit STREAM --NO_HEADER" + "-rit STREAM --NO_HEADER " +
" -o %s", "-o %s",
1, 1,
Arrays.asList("2cae3d16f9ed00b07d87e9c49272d877") Arrays.asList("2cae3d16f9ed00b07d87e9c49272d877")
); );
executeTest("testSimpleVCFStreaming", spec); executeTest("testSimpleVCFStreaming", spec);
tmpFifo.delete();
} }
@Test @Test
public void testVCFStreamingChain() throws IOException { 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). // 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",""); File tmpFifo = File.createTempFile("vcfstreaming","");
tmpFifo.deleteOnExit();
Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()}); Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()});
String testFile = validationDataLocation + "yri.trio.gatk.ug.head.vcf"; String testFile = validationDataLocation + "yri.trio.gatk.ug.head.vcf";
@ -104,5 +103,6 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
); );
executeTest("testVCFStreamingChain", selectTestSpec); executeTest("testVCFStreamingChain", selectTestSpec);
tmpFifo.delete();
} }
} }