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Removing parameters that were incorrectly copied over from RegenotypeVariants.

This commit is contained in:
Eric Banks 2014-02-08 23:24:46 -05:00
parent e9189cd471
commit abef6cfcb6
2 changed files with 3 additions and 7 deletions
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6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
View File

@ -166,11 +166,7 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
vcfWriter.writeHeader(vcfHeader);
// create the genotyping engine
final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
genotypingEngine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
genotypingEngine = new UnifiedGenotyperEngine(getToolkit(), new UnifiedArgumentCollection(), logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
// create the annotation engine
annotationEngine = new VariantAnnotatorEngine(Arrays.asList("none"), annotationsToUse, Collections.<String>emptyList(), this, getToolkit());

4
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
View File

@ -65,7 +65,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-20,000,000", b37KGReference),
1,
Arrays.asList("8fd26c30509b98372c2945405a1d7cc4"));
Arrays.asList("54487ea151c49d36a15eac8097a7e460"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@ -89,7 +89,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
1,
Arrays.asList("d0eb9046c24fa6a66ee20feff35457d4"));
Arrays.asList("9e6ef126d5e872e5b2a68c3d73471566"));
executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
}