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Merged bug fix from Stable into Unstable 

Conflicts:
	public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
This commit is contained in:
David Roazen 2011-10-11 12:03:51 -04:00
parent 0429b38021 24b72334b3
commit cfd0ac8410
2 changed files with 18 additions and 1 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -214,7 +214,13 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples);
// initialize the header
writer.writeHeader(new VCFHeader(getHeaderInfo(), samples)) ;
Set<VCFHeaderLine> headerInfo = getHeaderInfo();
// invoke initialize() method on each of the annotation classes, allowing them to add their own header lines
// and perform any necessary initialization/validation steps
annotationEngine.invokeAnnotationInitializationMethods(headerInfo);
writer.writeHeader(new VCFHeader(headerInfo, samples));
}
private Set<VCFHeaderLine> getHeaderInfo() {

11
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;
import java.io.File;
@ -293,4 +294,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
Arrays.asList("37d908a682ac269f8f19dec939ff5b01"));
executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4);
}
@Test
public void testSnpEffAnnotationRequestedWithoutRodBinding() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000 " +
"-A SnpEff",
1,
UserException.class);
executeTest("testSnpEffAnnotationRequestedWithoutRodBinding", spec);
}
}