89 lines
3.2 KiB
Java
Executable File
89 lines
3.2 KiB
Java
Executable File
package org.broadinstitute.sting.gatk.walkers;
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import org.broadinstitute.sting.WalkerTest;
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import org.testng.annotations.Test;
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import java.util.List;
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import java.util.ArrayList;
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/**
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* @author aaron
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* <p/>
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* Class VariantsToVCFIntegrationTest
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* <p/>
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* test(s) for the VariantsToVCF walker.
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*/
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public class VariantsToVCFIntegrationTest extends WalkerTest {
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@Test
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public void testVariantsToVCFUsingGeliInput() {
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List<String> md5 = new ArrayList<String>();
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md5.add("bd15d98adc76b5798e3bbeff3f936feb");
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-R " + b36KGReference +
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" -B:variant,GeliText " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
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" -T VariantsToVCF" +
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" -L 1:10,000,000-11,000,000" +
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" -sample NA123AB" +
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" -o %s" +
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" -NO_HEADER",
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1, // just one output file
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md5);
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executeTest("testVariantsToVCFUsingGeliInput #1", spec).getFirst();
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}
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@Test
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public void testGenotypesToVCFUsingGeliInput() {
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List<String> md5 = new ArrayList<String>();
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md5.add("acd15d3f85bff5b545bc353e0e23cc6e");
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-R " + b36KGReference +
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" -B:variant,GeliText " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" +
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" -T VariantsToVCF" +
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" -L 1:10,000,000-11,000,000" +
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" -sample NA123AB" +
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" -o %s" +
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" -NO_HEADER",
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1, // just one output file
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md5);
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executeTest("testVariantsToVCFUsingGeliInput #2", spec).getFirst();
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}
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@Test
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public void testGenotypesToVCFUsingHapMapInput() {
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List<String> md5 = new ArrayList<String>();
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md5.add("6f34528569f8cf5941cb365fa77288c1");
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-R " + b36KGReference +
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" -B:variant,HapMap " + validationDataLocation + "rawHapMap.yri.chr1.txt" +
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" -T VariantsToVCF" +
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" -L 1:1-1,000,000" +
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" -o %s" +
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" -NO_HEADER",
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1, // just one output file
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md5);
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executeTest("testVariantsToVCFUsingHapMapInput", spec).getFirst();
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}
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@Test
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public void testGenotypesToVCFUsingVCFInput() {
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List<String> md5 = new ArrayList<String>();
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md5.add("d8316fc1b9d8e954a58940354119a32e");
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-R " + b36KGReference +
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" -B:variant,VCF " + validationDataLocation + "complexExample.vcf4" +
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" -T VariantsToVCF" +
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" -o %s" +
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" -NO_HEADER",
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1, // just one output file
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md5);
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executeTest("testVariantsToVCFUsingVCFInput", spec).getFirst();
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}
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}
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