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Added integration test for ValidationSiteSelector, correct MD5's

This commit is contained in:
Guillermo del Angel 2012-03-26 16:39:55 -04:00
parent 8f0828daa6
commit 1a2a4848e8
1 changed files with 90 additions and 0 deletions
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90
public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java 100644
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package org.broadinstitute.sting.gatk.walkers.validation;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import java.util.Arrays;
/**
* Created by IntelliJ IDEA.
* User: delangel
* Date: 3/26/12
* Time: 3:29 PM
* To change this template use File | Settings | File Templates.
*/
public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
public static String baseTestString(String args) {
return "-T ValidationSiteSelector -R " + b36KGReference + " -L 1 -o %s -NO_HEADER -numSites 100 " + args;
}
private static String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
private static String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
private static String samplePrefix = " -sf " + samplesFile;
private static String freqUnif = " --frequencySelectionMode UNIFORM ";
private static String freqAF = " --frequencySelectionMode KEEP_AF_SPECTRUM ";
private static String sampleNone = " -sampleMode NONE ";
private static String sampleGT = samplePrefix+" -sampleMode POLY_BASED_ON_GT ";
private static String sampleGL = samplePrefix+" -sampleMode POLY_BASED_ON_GL -samplePNonref 0.95";
@Test(enabled=true)
public void testNoSampleSelectionFreqUniform() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleNone + freqUnif + "--variant " + testfile),
1,
Arrays.asList("d49baeb8000a426c172ce1d81eb37963")
);
executeTest("testNoSampleSelectionFreqUniform--" + testfile, spec);
}
@Test(enabled=true)
public void testNoSampleSelectionFreqAF() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleNone + freqAF + "--variant " + testfile),
1,
Arrays.asList("0fb0d015d462c34514fc7e96beea5f56")
);
executeTest("testNoSampleSelectionFreqAF--" + testfile, spec);
}
@Test(enabled=true)
public void testPolyGTFreqUniform() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleGT + freqUnif + "--variant " + testfile),
1,
Arrays.asList("0672854299d42ea8af906976a3849ae6")
);
executeTest("testPolyGTFreqUniform--" + testfile, spec);
}
@Test(enabled=true)
public void testPolyGTFreqAF() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleGT + freqAF + "--variant " + testfile),
1,
Arrays.asList("5bdffda1a063d0bddd6b236854ec627d")
);
executeTest("testPolyGTFreqAF--" + testfile, spec);
}
@Test(enabled=true)
public void testPolyGLFreqAF() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleGL + freqAF + "--variant " + testfile),
1,
Arrays.asList("35ef16aa41303606a4b94f7b88bd9aa8")
);
executeTest("testPolyGLFreqAF--" + testfile, spec);
}
}