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Adding integration test that uses the -V:dbsnp binding to make sure it won't fail later on if someone messes with Tribble.

This commit is contained in:
Eric Banks 2011-09-21 22:43:31 -04:00
parent 8f8b59a932
commit b8ea9ceb68
1 changed files with 10 additions and 10 deletions
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20
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
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@ -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), baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
1, 1,
Arrays.asList("d18516c1963802e92cb9e425c0b75fd6") Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
); );
@ -30,7 +30,7 @@ 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(
"-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s -NO_HEADER -xl_sn A -xl_sf " + samplesFile + " --variant:VCF3 " + testfile, "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s -NO_HEADER -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile,
1, 1,
Arrays.asList("730f021fd6ecf1d195dabbee2e233bfd") Arrays.asList("730f021fd6ecf1d195dabbee2e233bfd")
); );
@ -43,7 +43,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
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), baseTestString(" -sn A -sn B -sn C --variant " + testfile),
1, 1,
Arrays.asList("b74038779fe6485dbb8734ae48178356") Arrays.asList("b74038779fe6485dbb8734ae48178356")
); );
@ -56,7 +56,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
String testFile = validationDataLocation + "NA12878.hg19.example1.vcf"; String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant:VCF " + b37hapmapGenotypes + " -disc:VCF " + testFile + " -o %s -NO_HEADER", "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s -NO_HEADER",
1, 1,
Arrays.asList("78e6842325f1f1bc9ab30d5e7737ee6e") Arrays.asList("78e6842325f1f1bc9ab30d5e7737ee6e")
); );
@ -69,7 +69,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
String testFile = validationDataLocation + "NA12878.hg19.example1.vcf"; String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc:VCF " + b37hapmapGenotypes + " --variant " + testFile + " -o %s -NO_HEADER", "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc " + b37hapmapGenotypes + " --variant " + testFile + " -o %s -NO_HEADER",
1, 1,
Arrays.asList("d2ba3ea30a810f6f0fbfb1b643292b6a") Arrays.asList("d2ba3ea30a810f6f0fbfb1b643292b6a")
); );
@ -90,16 +90,16 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testVariantTypeSelection--" + testFile, spec); executeTest("testVariantTypeSelection--" + testFile, spec);
} }
@Test(enabled=false) @Test
public void testRemovePLs() { public void testUsingDbsnpName() {
String testFile = validationDataLocation + "combine.3.vcf"; String testFile = validationDataLocation + "combine.3.vcf";
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s -NO_HEADER", "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s -NO_HEADER",
1, 1,
Arrays.asList("") Arrays.asList("167a1265df820978a74c267df44d5c43")
); );
executeTest("testWithPLs--" + testFile, spec); executeTest("testUsingDbsnpName--" + testFile, spec);
} }
} }