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Adding integration test to cover sample exclusion

This commit is contained in:
Eric Banks 2011-08-17 22:40:09 -04:00
parent a7b70e6bb4
commit b75a1807e3
1 changed files with 17 additions and 3 deletions
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20
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
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@ -7,7 +7,7 @@ import java.util.Arrays;
public class SelectVariantsIntegrationTest extends WalkerTest { public class SelectVariantsIntegrationTest extends WalkerTest {
public static String baseTestString(String args) { public static String baseTestString(String args) {
return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s" + args; return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s -NO_HEADER" + args;
} }
@Test @Test
@ -16,7 +16,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant:VCF3 " + testfile + " -NO_HEADER"), baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant:VCF3 " + testfile),
1, 1,
Arrays.asList("d18516c1963802e92cb9e425c0b75fd6") Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
); );
@ -24,12 +24,26 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testComplexSelection--" + testfile, spec); executeTest("testComplexSelection--" + testfile, spec);
} }
@Test
public void testSampleExclusion() {
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s -NO_HEADER -xl_sn A -xl_sf " + samplesFile + " --variant:VCF3 " + testfile,
1,
Arrays.asList("730f021fd6ecf1d195dabbee2e233bfd")
);
executeTest("testSampleExclusion--" + testfile, spec);
}
@Test @Test
public void testRepeatedLineSelection() { public void testRepeatedLineSelection() {
String testfile = validationDataLocation + "test.dup.vcf"; String testfile = validationDataLocation + "test.dup.vcf";
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -sn B -sn C --variant:VCF3 " + testfile + " -NO_HEADER"), baseTestString(" -sn A -sn B -sn C --variant:VCF3 " + testfile),
1, 1,
Arrays.asList("b74038779fe6485dbb8734ae48178356") Arrays.asList("b74038779fe6485dbb8734ae48178356")
); );