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

No more VC integration tests. All tests are now unit tests

This commit is contained in:
Mark DePristo 2011-11-17 15:33:09 -05:00
parent 23359d1c6c
commit 02f22cc9f8
1 changed files with 0 additions and 65 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

65
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
View File

@ -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);
}
}