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Got tired of waiting for Kiran to fix the build: updated NewVariantEval -> 

VariantEval.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5161 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-02-01 15:32:39 +00:00
parent 96241c6637
commit 7d89ce820b
1 changed files with 4 additions and 4 deletions
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8
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -9,7 +9,7 @@ import java.util.HashMap;
import java.util.Map;
public class VariantEvalIntegrationTest extends WalkerTest {
private static String cmdRoot = "-T NewVariantEval" +
private static String cmdRoot = "-T VariantEval" +
" -R " + b36KGReference;
private static String root = cmdRoot +
@ -104,7 +104,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
// @Test
// public void testVEGenomicallyAnnotated() {
// String vecmd = "-T NewVariantEval" +
// String vecmd = "-T VariantEval" +
// " -R " + b36KGReference +
// " -L 21" +
// " -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
@ -132,7 +132,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T NewVariantEval -R "+b36KGReference+" -o %s -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";
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -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("929e4ec46fb6957c29803531322bb35e"));
//executeTestParallel("testACDiscordanceAtAC1EvalAC2Comp",spec);
executeTest("testCompVsEvalAC",spec);
@ -144,7 +144,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testTranches() {
String extraArgs = "-T NewVariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -tf " + testDir + "tranches.6.txt";
String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -tf " + testDir + "tranches.6.txt";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("68044a69f03ba4cc11d2061cc96e9eb5"));
//executeTestParallel("testTranches",spec);
executeTest("testTranches",spec);