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re-enabling PlinkToVCF integration tests 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2964 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-09 17:35:49 +00:00
parent 5a20bf0e64
commit e5475a7ba9
2 changed files with 26 additions and 27 deletions
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26
java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCFIntegrationTest.java 100644
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@ -0,0 +1,26 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantstovcf;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
public class PlinkToVCFIntegrationTest extends WalkerTest {
@Test
public void testSNPs() {
String testPedFile = validationDataLocation + "Sequenom_Test_File.txt";
String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T PlinkToVCF -B input,Plink,"+testPedFile+" -vcf %s";
WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
Arrays.asList("02dcb683db503599efed0b76daa8fcba"));
executeTest("Test SNPs", spec);
}
@Test
public void testIndels() {
String testPedFile = validationDataLocation + "pilot2_indel_validation.renamed.ped";
String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T PlinkToVCF -B input,Plink,"+testPedFile+" -vcf %s";
WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
Arrays.asList("e72c0ab95b279a4d39cc14d40770a801"));
executeTest("Test Indels", spec);
}
}

27
java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCFIntegrationTest.java
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@ -1,27 +0,0 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantstovcf;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.io.File;
import java.util.Arrays;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: Jan 11, 2010
* Time: 11:30:59 AM
* To change this template use File | Settings | File Templates.
*/
public class SequenomToVCFIntegrationTest extends WalkerTest {
//@Test
public void testSequenomToVCFWithoutSmartHardy() {
String testMD5 = "a16ce402ce4492c8c0552073c0a8bdf5";
String testPedFile = "/humgen/gsa-hpprojects/GATK/data/Validation_Data/Sequenom_Test_File.txt";
String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -L 1:1000000-2000000 "+
"-T PlinkToVCF -b36contig -ns 10 -B input,Plink,"+testPedFile+" -vcf %s";
WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs,1, Arrays.asList(testMD5));
List<File> result = executeTest("TestSequenomToVCFNoSmartHardy",spec).getFirst();
}
}