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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2012-10-31 21:28:27 -04:00
parent 96344c6b62 f8af8a2355
commit 881c843307
2 changed files with 35 additions and 0 deletions
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0
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java → protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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35
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLiteIntegrationTest.java 100755
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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;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
// ********************************************************************************** //
// Note that this class also serves as an integration test for the VariantAnnotator! //
// ********************************************************************************** //
public class UnifiedGenotyperLiteIntegrationTest extends WalkerTest {
private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
// --------------------------------------------------------------------------------------------------------------
//
// testing contamination down-sampling gets ignored
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testContaminationDownsampling() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("9addd225a985178339a0c49dc5fdc220"));
executeTest("test contamination_percentage_to_filter gets ignored", spec);
}
}