diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index 30cdbee36..5e674d6c2 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -167,36 +167,6 @@ public class SelectVariantsIntegrationTest extends WalkerTest { executeTest("testNoGTs--" + testFile, spec); } - @Test(enabled = false) - public void testParallelization2() { - String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; - String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; - WalkerTestSpec spec; - - spec = new WalkerTestSpec( - baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 2"), - 1, - Arrays.asList("433eccaf1ac6e6be500ef0984a5d8d8b") - ); - spec.disableShadowBCF(); - executeTest("testParallelization (2 threads)--" + testfile, spec); - } - - @Test(enabled = false) - public void testParallelization4() { - String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; - String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; - WalkerTestSpec spec; - spec = new WalkerTestSpec( - baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 4"), - 1, - Arrays.asList("433eccaf1ac6e6be500ef0984a5d8d8b") - ); - spec.disableShadowBCF(); - - executeTest("testParallelization (4 threads)--" + testfile, spec); - } - @Test public void testSelectFromMultiAllelic() { String testfile = privateTestDir + "multi-allelic.bi-allelicInGIH.vcf"; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java new file mode 100755 index 000000000..ff3982d24 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java @@ -0,0 +1,59 @@ +package org.broadinstitute.sting.gatk.walkers.variantutils; + +import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.util.Arrays; + +public class SelectVariantsParallelIntegrationTest extends WalkerTest { + + private class ParallelSelectTestProvider extends TestDataProvider { + final String reference; + final String args; + final String md5; + final int nt; + + private ParallelSelectTestProvider(final String reference, final String args, final String md5, final int nt) { + super(ParallelSelectTestProvider.class); + this.reference = reference; + this.args = args; + this.md5 = md5; + this.nt = nt; + } + + public final String getCmdLine() { + return "-T SelectVariants -R " + reference + " -o %s -L 1 --no_cmdline_in_header -nt " + nt + " " + args; + } + + public String toString() { + return String.format("ParallelSelectVariants nt=%d args=%s", nt, args); + } + } + + @DataProvider(name = "ParallelSelectTest") + public Object[][] makeParallelSelectTestProvider() { + for ( int nt : Arrays.asList(1, 2, 4) ) { + { // original MAF test + String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; + String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; + String args = " -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile; + new ParallelSelectTestProvider(b36KGReference, args, "4386fbb258dcef4437495a37f5a83c53", nt); + } + { // new tests on b37 using testdir VCF + final String testfile = privateTestDir + "NA12878.hg19.example1.vcf"; + final String args = "-select 'DP > 30' -V " + testfile; + new ParallelSelectTestProvider(b37KGReference, args, "c64b45a14d41b1e5cddbe036b47e7519", nt); + } + } + + return ParallelSelectTestProvider.getTests(ParallelSelectTestProvider.class); + } + + @Test(dataProvider = "ParallelSelectTest") + public void testParallelSelectTestProvider(final ParallelSelectTestProvider cfg) { + final WalkerTestSpec spec = new WalkerTestSpec( cfg.getCmdLine(), 1, Arrays.asList(cfg.md5) ); + executeTest(cfg.toString(), spec); + } +}