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Continuing the epic fail, some of our existing integration tests were wrong because of the lazy loading failure. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5712 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-29 17:54:41 +00:00
parent ab9ffb1a74
commit deed7c47a1
2 changed files with 7 additions and 7 deletions
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2
java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
View File

@ -72,7 +72,7 @@ public class BeagleIntegrationTest extends WalkerTest {
"-B:beagleR2,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
"-B:beagleProbs,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
"-B:beaglePhased,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
"-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("e09d2cba18ab5c571e563085296cd514"));
"-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("24b88ef8cdf6e347daab491f0256be5a"));
executeTest("testBeagleChangesSitesToRef",spec);
}

12
java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testNoAction() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("c9f49679f600c52e624c74cf65fd0a39"));
Arrays.asList("4cc077eb3d343e6b7ba12bff86ebe347"));
executeTest("test no action", spec);
}
@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testClusteredSnps() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -window 10 -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("559021b518503df2ca1cc5cd18642248"));
Arrays.asList("ada5540bb3d9b6eb8f1337ba01e90a94"));
executeTest("test clustered SNPs", spec);
}
@ -32,7 +32,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testMask() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -mask foo -B:mask,VCF " + validationDataLocation + "vcfexample2.vcf -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("467480f5c2e840b68d8ef591f1c562c7"));
Arrays.asList("b0fcac4af3526e3b2a37602ab4c0e6ae"));
executeTest("test mask", spec);
}
@ -40,7 +40,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilter1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("b48b5965d05f2d0f02c6f7261e67e9d2"));
Arrays.asList("7a40795147cbfa92941489d7239aad92"));
executeTest("test filter #1", spec);
}
@ -48,7 +48,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilter2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("42bfb7df7a83e5007a1d1da523a64d75"));
Arrays.asList("e9dd4991b1e325847c77d053dfe8ee54"));
executeTest("test filter #2", spec);
}
@ -56,7 +56,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilterWithSeparateNames() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("c2b1d53a50d99229b351470a39692eb6"));
Arrays.asList("9ded2cce63b8d97550079047051d80a3"));
executeTest("test filter with separate names #2", spec);
}