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

Re-enabling multi-threaded integration tests. To make this work, downsampling and annotations are disabled for this test so that we don't have randomization issues for it based on which shards get executed first. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5597 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-08 03:07:39 +00:00
parent 1763a41e94
commit cd61ef7169
1 changed files with 8 additions and 31 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

39
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -100,26 +100,29 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
@Test (enabled = false)
@Test
public void testParallelization() {
String md5 = "7e51ad5e76b8440cbf26373df83a8f41";
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
String md5 = "f56fdf5c6a2db85031a3cece37e12a56";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
Arrays.asList(md5));
executeTest("test parallelization (single thread)", spec1);
GenomeAnalysisEngine.resetRandomGenerator();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 2", 1,
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 2", 1,
Arrays.asList(md5));
executeTest("test parallelization (2 threads)", spec2);
GenomeAnalysisEngine.resetRandomGenerator();
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 4", 1,
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 4", 1,
Arrays.asList(md5));
executeTest("test parallelization (4 threads)", spec3);
}
@ -279,32 +282,6 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
// Indel parallelization
//@Test
// todo - test fails because for some reason when including -nt we get "PASS" instead of . in filter fields
public void testIndelParallelization() {
String md5 = "599220ba0cc5d8a32e4952fca85fd080";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation +
"NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -glm INDEL -o %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList(md5));
executeTest("test indel caller parallelization (single thread)", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation +
"NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -glm INDEL -o %s -L 1:10,000,000-10,100,000 -nt 2", 1,
Arrays.asList(md5));
executeTest("test indel caller parallelization (2 threads)", spec2);
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation +
"NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -glm INDEL -o %s -L 1:10,000,000-10,100,000 -nt 4", 1,
Arrays.asList(md5));
executeTest("test indel caller parallelization (4 threads)", spec3);
}
// todo - feature not yet fully working with indels
//@Test
public void testWithIndelAllelesPassedIn() {