diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java deleted file mode 100755 index 67fe7d012..000000000 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java +++ /dev/null @@ -1,65 +0,0 @@ - - -package org.broadinstitute.sting.utils.variantcontext; - -import org.broadinstitute.sting.WalkerTest; -import org.testng.annotations.DataProvider; -import org.testng.annotations.Test; - -import java.util.HashMap; -import java.util.Map; -import java.util.Arrays; - -public class VariantContextIntegrationTest extends WalkerTest { - private static String cmdRoot = "-T TestVariantContext" + - " -R " + b36KGReference; - - private static String root = cmdRoot + - " -L 1:1-1,000,000 -V " + b36dbSNP129; - - private static final class VCITTest extends TestDataProvider { - String args, md5; - - private VCITTest(final String args, final String md5) { - super(VCITTest.class); - this.args = args; - this.md5 = md5; - } - } - - @DataProvider(name = "VCITTestData") - public Object[][] createVCITTestData() { - new VCITTest("--printPerLocus", "e9d0f1fe80659bb55b40aa6c3a2e921e"); - new VCITTest("--printPerLocus --onlyContextsOfType SNP", "0e620db3e45771df42c54a9c0ae4a29f"); - new VCITTest("--printPerLocus --onlyContextsOfType INDEL", "b725c204fefe3814644d50e7c20f9dfe"); - new VCITTest("--printPerLocus --onlyContextsOfType MIXED", "3ccc33f496a1718df55722d11cc14334"); - new VCITTest("--printPerLocus --onlyContextsOfType NO_VARIATION", "39335acdb34c8a2af433dc50d619bcbc"); - new VCITTest("--printPerLocus --takeFirstOnly", "3a45561da042b2b44b6a679744f16103"); - new VCITTest("--printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "4746f269ecc377103f83eb61cc162c39"); - new VCITTest("--printPerLocus --onlyContextsStartinAtCurrentPosition", "2749e3fae458650a85a2317e346dc44c"); - new VCITTest("--printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "9bd48c2a40813023e29ffaa23d59d382"); - - return VCITTest.getTests(VCITTest.class); - } - - @Test(dataProvider = "VCITTestData") - public void testConversionSelection(VCITTest test) { - String extraArgs = test.args; - String md5 = test.md5; - - WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s", - 1, // just one output file - Arrays.asList(md5)); - executeTest("testSelectors", spec); - } - - @Test - public void testToVCF() { - // this really just tests that we are seeing the same number of objects over all of chr1 - - WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -V:VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s", - 2, // just one output file - Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "ff91731213fd0bbdc200ab6fd1c93e63")); - executeTest("testToVCF", spec); - } -}