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Fixed integration test to reflect changes regarding when comp tracks got subset to fewer samples and whether no-call sites would get pulled in for comp tracks. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5393 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-03-07 20:25:57 +00:00
parent 73e43d8d2c
commit 43056d0188
1 changed files with 11 additions and 11 deletions
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22
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -334,7 +334,7 @@ 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("4ae87d76a3b39cf0b80221f3bd681839"));
1, Arrays.asList("9e74d649fcf1c884b324f0818e1d7395"));
executeTestParallel("testSelect1", spec);
//executeTest("testSelect1", spec);
}
@ -355,7 +355,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
for (String vcfFile : vcfFiles) {
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
1,
Arrays.asList("1387fcf8d5c53ff2c820fe79cc999bcf"));
Arrays.asList("86de930ab857e27717c80b11594808f3"));
executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
//executeTest("testVEGenotypeConcordance" + vcfFile, spec);
}
@ -365,8 +365,8 @@ 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", "b82f1ad442d354a5ed3c18ecef93553e");
expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "dc3d34f5a03890217d1f548027a82028");
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");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
@ -389,9 +389,9 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
expectations.put("", "c3936ef2e7af52019ade05461fbf4180");
expectations.put(" -knownName comp_hapmap -knownName dbsnp", "e19bd1bc89463e558fa3b83e65f55ca5");
expectations.put(" -knownName comp_hapmap", "831d69ec830836f7d2ac8310713f1691");
expectations.put("", "48fcd7d9f3c8e347c70d7692c4b3cbff");
expectations.put(" -knownName comp_hapmap -knownName dbsnp", "308948e0e227425d73e35a6702bfefcb");
expectations.put(" -knownName comp_hapmap", "6f1383f3ea5b741215e8f7cbfcb47fb1");
for (String tests : testsEnumerations) {
for (Map.Entry<String, String> entry : expectations.entrySet()) {
String extraArgs2 = entry.getKey();
@ -409,7 +409,7 @@ 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("132e0825d1ed6e54963da94784cf7803"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("3199177faa347fe3a78de17b83afd909"));
executeTestParallel("testCompVsEvalAC",spec);
//executeTest("testCompVsEvalAC",spec);
}
@ -429,7 +429,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompOverlap() {
String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals -B:comphapmap,vcf " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf -B:eval,vcf " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("e8b5561eb60ea98a9be4a45abee00e07"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("70aa420929de7f888a6f48c2d01bbcda"));
executeTestParallel("testCompOverlap",spec);
//executeTest("testCompOverlap",spec);
}
@ -444,7 +444,7 @@ 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("5d0d89c7cbcc7887e34447cee70c5bae"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2ea5334cf0b004e0a6119a5b653bde4c"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@ -458,7 +458,7 @@ 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("8dec8f384852876ba8ec4943ff953d2d"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("50fb57dddf7040a62e3befba30c5cb22"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}