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Adding integration test for file with no GTs. Also updated md5 for one other test (since we no longer print out 'NaN' for the AF).

This commit is contained in:
Eric Banks 2012-02-27 15:09:56 -05:00
parent 998ed8fff3
commit 52871187d7
1 changed files with 14 additions and 1 deletions
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15
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
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@ -45,7 +45,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -sn B -sn C --variant " + testfile), baseTestString(" -sn A -sn B -sn C --variant " + testfile),
1, 1,
Arrays.asList("b74038779fe6485dbb8734ae48178356") Arrays.asList("5085a2f8cddfeae9f6274f905025184f")
); );
executeTest("testRepeatedLineSelection--" + testfile, spec); executeTest("testRepeatedLineSelection--" + testfile, spec);
@ -129,6 +129,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec); executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec);
} }
@Test
public void testNoGTs() {
String testFile = validationDataLocation + "vcf4.1.example.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s -NO_HEADER",
1,
Arrays.asList("f17885e5cbd5387edb99112047ea43c1")
);
executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec);
}
@Test @Test
public void testParallelization() { public void testParallelization() {
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";