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fixing the build \o/ 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5767 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-05-05 00:57:49 +00:00
parent 8ad547e6c2
commit 3882d1b9c0
1 changed files with 9 additions and 9 deletions
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18
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -336,7 +336,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String extraArgs = "-L 1:1-10,000,000";
for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
1, Arrays.asList("9e74d649fcf1c884b324f0818e1d7395"));
1, Arrays.asList("ca71324abf5659964c8f9e28b8fdbb28"));
executeTestParallel("testSelect1", spec);
//executeTest("testSelect1", spec);
}
@ -367,8 +367,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testVESimple() {
HashMap<String, String> expectations = new HashMap<String, String>();
expectations.put("-L 1:1-10,000,000 -ST CpG", "9784b1fc319e856ad84678b6c8a4c15c");
expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "374c06e9ba8ca3496698b3f95e241b82");
expectations.put("-L 1:1-10,000,000 -ST CpG", "c74067360656519f769f805d6e1ef36b");
expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "0fe151e00ab35f3b95d4fea651592ec3");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
@ -391,9 +391,9 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
expectations.put("", "48fcd7d9f3c8e347c70d7692c4b3cbff");
expectations.put(" -knownName comp_hapmap -knownName dbsnp", "308948e0e227425d73e35a6702bfefcb");
expectations.put(" -knownName comp_hapmap", "6f1383f3ea5b741215e8f7cbfcb47fb1");
expectations.put("", "700eba07bac9fba4ed963bbbdcab0e29");
expectations.put(" -knownName comp_hapmap -knownName dbsnp", "c2464d5613072fb326ebffcf3078ae31");
expectations.put(" -knownName comp_hapmap", "0912f35a4c4179ff93b152d8c4e009e2");
for (String tests : testsEnumerations) {
for (Map.Entry<String, String> entry : expectations.entrySet()) {
String extraArgs2 = entry.getKey();
@ -411,7 +411,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("06cd5618ec23fe83a0ddb2a3e8622a16"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("e68272d2f3b7a6439c4949cf0e34beeb"));
executeTestParallel("testCompVsEvalAC",spec);
//executeTest("testCompVsEvalAC",spec);
}
@ -446,7 +446,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -D " + dbsnp +
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2ea5334cf0b004e0a6119a5b653bde4c"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("923af856d04042c0ee9d01aa9eb8675a"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@ -460,7 +460,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("50fb57dddf7040a62e3befba30c5cb22"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("45c08af95777e1eee3e9acbf136a8b6b"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}