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Commented out, because these fail the now removed dbSNP conversion.

This commit is contained in:
Mark DePristo 2011-08-01 13:34:25 -04:00
parent 4f8d830960
commit f69bff5dd6
1 changed files with 34 additions and 21 deletions
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55
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
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@ -3,6 +3,7 @@
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;
@ -17,30 +18,42 @@ public class VariantContextIntegrationTest extends WalkerTest {
" -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
static HashMap<String, String> expectations = new HashMap<String, String>();
static {
expectations.put("-L 1:1-10000 --printPerLocus", "e4ee2eaa3114888e918a1c82df7a027a");
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "5b5635e4877d82e8a27d70dac24bda2f");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "ceced3f270b4fe407ee83bc9028becde");
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "9a9b9e283553c28bf58de1cafa38fe92");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "2097e32988d603d3b353b50218c86d3b");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "033bd952fca048fe1a4f6422b57ab2ed");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "5e40980c02797f90821317874426a87a");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "e5a00766f8c1ff9cf92310bafdec3126");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType NO_VARIATION", "39335acdb34c8a2af433dc50d619bcbc");
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;
}
}
@Test
public void testConversionSelection() {
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
String md5 = entry.getValue();
@DataProvider(name = "VCITTestData")
public Object[][] createVCITTestData() {
new VCITTest("-L 1:1-10000 --printPerLocus", "e4ee2eaa3114888e918a1c82df7a027a");
new VCITTest("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "2097e32988d603d3b353b50218c86d3b");
new VCITTest("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "033bd952fca048fe1a4f6422b57ab2ed");
new VCITTest("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "e5a00766f8c1ff9cf92310bafdec3126");
new VCITTest("-L 1:1-10000 --printPerLocus --onlyContextsOfType NO_VARIATION", "39335acdb34c8a2af433dc50d619bcbc");
WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s",
1, // just one output file
Arrays.asList(md5));
executeTest("testDbSNPAndVCFConversions", spec);
}
// TODO : Eric, these are bad because the conversion fails
//new VCITTest("-L 1:1-10000 --printPerLocus --takeFirstOnly", "5b5635e4877d82e8a27d70dac24bda2f");
//new VCITTest("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "5e40980c02797f90821317874426a87a");
//new VCITTest("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "ceced3f270b4fe407ee83bc9028becde");
//new VCITTest("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "9a9b9e283553c28bf58de1cafa38fe92");
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("testDbSNPAndVCFConversions", spec);
}
@Test