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Added Integration tests for Phasing by Transmission

This commit is contained in:
Laurent Francioli 2011-11-14 10:47:51 +01:00
parent 34acf8b978
commit 6881d4800c
1 changed files with 115 additions and 7 deletions
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122
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
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@ -6,23 +6,131 @@ import org.testng.annotations.Test;
import java.util.Arrays;
public class PhaseByTransmissionIntegrationTest extends WalkerTest {
private static String phaseByTransmissionTestDataRoot = validationDataLocation + "/PhaseByTransmission";
private static String fundamentalTestVCF = phaseByTransmissionTestDataRoot + "/" + "FundamentalsTest.unfiltered.vcf";
private static String phaseByTransmissionTestDataRoot = validationDataLocation + "PhaseByTransmission/";
private static String goodFamilyFile = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.goodFamilies.ped";
private static String TNTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.TN.vcf";
private static String TPTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.TP.vcf";
private static String FPTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.FP.vcf";
private static String SpecialTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.Special.vcf";
//Tests using PbT on all genotypes with default parameters
//And all reporting options
@Test
public void testBasicFunctionality() {
public void testTrueNegativeMV() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T PhaseByTransmission",
"-NO_HEADER",
"-R " + b37KGReference,
"--variant " + fundamentalTestVCF,
"-f NA12892+NA12891=NA12878",
"--variant " + TNTest,
"-ped "+ goodFamilyFile,
"-L 1:10109-10315",
"-mvf %s",
"-o %s"
),
2,
Arrays.asList("16fefda693156eadf1481fd9de23facb","9418a7a6405b78179ca13a67b8bfcc14")
);
executeTest("testTrueNegativeMV", spec);
}
@Test
public void testTruePositiveMV() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T PhaseByTransmission",
"-NO_HEADER",
"-R " + b37KGReference,
"--variant " + TPTest,
"-ped "+ goodFamilyFile,
"-L 1:10109-10315",
"-mvf %s",
"-o %s"
),
2,
Arrays.asList("14cf1d21a54d8b9fb506df178b634c56","efc66ae3d036715b721f9bd35b65d556")
);
executeTest("testTruePositiveMV", spec);
}
@Test
public void testFalsePositiveMV() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T PhaseByTransmission",
"-NO_HEADER",
"-R " + b37KGReference,
"--variant " + FPTest,
"-ped "+ goodFamilyFile,
"-L 1:10109-10315",
"-mvf %s",
"-o %s"
),
2,
Arrays.asList("f9b0fae9fe1e0f09b883a292b0e70a12","398724bc1e65314cc5ee92706e05a3ee")
);
executeTest("testFalsePositiveMV", spec);
}
@Test
public void testSpecialCases() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T PhaseByTransmission",
"-NO_HEADER",
"-R " + b37KGReference,
"--variant " + SpecialTest,
"-ped "+ goodFamilyFile,
"-L 1:10109-10315",
"-mvf %s",
"-o %s"
),
2,
Arrays.asList("b8d1aa3789ce77b45430c62d13ee3006","a1a333e08fafb288cda0e7711909e1c3")
);
executeTest("testSpecialCases", spec);
}
//Test using a different prior
//Here the FP file is used but as the prior is lowered, 3 turn to TP
@Test
public void testPriorOption() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T PhaseByTransmission",
"-NO_HEADER",
"-R " + b37KGReference,
"--variant " + FPTest,
"-ped "+ goodFamilyFile,
"-L 1:10109-10315",
"-prior 1e-4",
"-mvf %s",
"-o %s"
),
2,
Arrays.asList("7201ce7cc47db5840ac6b647709f7c33","c11b5e7cd7459d90d0160f917eff3b1e")
);
executeTest("testPriorOption", spec);
}
//Test when running without MV reporting option
//This is the exact same test file as FP but should not generate a .mvf file
@Test
public void testMVFileOption() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T PhaseByTransmission",
"-NO_HEADER",
"-R " + b37KGReference,
"--variant " + FPTest,
"-ped "+ goodFamilyFile,
"-L 1:10109-10315",
"-o %s"
),
1,
Arrays.asList("")
Arrays.asList("398724bc1e65314cc5ee92706e05a3ee")
);
executeTest("testBasicFunctionality", spec);
executeTest("testMVFileOption", spec);
}
}