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Merge pull request #32 from broadinstitute/yf_per-sample-downsampling_GSA_765 

Fixed md5s for the per-sample downsampling IntegrationTests that were disabled.
This commit is contained in:
depristo 2013-02-13 10:08:11 -08:00
parent 961f2533a5 6d12e5a54f
commit 357d196dad
1 changed files with 43 additions and 10 deletions
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53
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java
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@ -47,15 +47,18 @@
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.util.Arrays;
import java.util.Random;
public class BiasedDownsamplingIntegrationTest extends WalkerTest {
private final static String baseCommand1 = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
private final static String baseCommand2 = "-T UnifiedGenotyper -R " + hg19Reference + " --no_cmdline_in_header -glm BOTH -L 20:1,000,000-5,000,000";
private final static String baseCommand3 = "-T UnifiedGenotyper -R " + hg19Reference + " --no_cmdline_in_header -glm BOTH -L 20:4,000,000-5,000,000";
private final String ArtificalBAMLocation = privateTestDir + "ArtificallyContaminatedBams/";
// --------------------------------------------------------------------------------------------------------------
@ -206,6 +209,40 @@ public class BiasedDownsamplingIntegrationTest extends WalkerTest {
}
private void testPerSampleEqualsFlat(final String bam1, final String bam2, final String persampleFile, final Double downsampling, final String md5) {
final String command = baseCommand3 + " -I " + ArtificalBAMLocation + bam1 + " -I " + ArtificalBAMLocation + bam2 + " -o %s ";
WalkerTestSpec spec = new WalkerTestSpec( command +" -contaminationFile " + persampleFile, 1, Arrays.asList(md5));
final Random rnd = GenomeAnalysisEngine.getRandomGenerator();
rnd.setSeed(123451); // so that the two test cases have a hope of giving the same result
executeTest("test contamination on Artificial Contamination, with per-sample file on " + bam1 + " and " + bam2 + " with " + persampleFile, spec);
spec = new WalkerTestSpec(command + "-contamination " + downsampling.toString(), 1, Arrays.asList(md5));
rnd.setSeed(123451); // so that the two test cases have a hope of giving the same result
executeTest("test contamination on Artificial Contamination, with flat contamination on " + bam1 + " and " + bam2 + " with " + downsampling.toString(), spec);
}
// verify that inputing a file with an effectively flat contamination level is equivalent to handing in a flat contamination level
@Test
public void testPerSampleEqualsFlatContaminationCase1() {
testPerSampleEqualsFlat("NA11918.with.2.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", ArtificalBAMLocation + "contamination.case.6.txt", 0.0, "");
}
@Test
public void testPerSampleEqualsFlatContaminationCase2() {
testPerSampleEqualsFlat("NA11918.with.2.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", ArtificalBAMLocation + "contamination.case.7.txt", 0.15, "");
}
@Test
public void testPerSampleEqualsFlatContaminationCase3() {
testPerSampleEqualsFlat("NA11918.with.2.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", ArtificalBAMLocation + "contamination.case.8.txt", 0.3, "");
}
// --------------------------------------------------------------------------------------------------------------
//
// testing HaplotypeCaller Contamination Removal
@ -244,23 +281,19 @@ public class BiasedDownsamplingIntegrationTest extends WalkerTest {
executeTest("HC test contamination on Artificial Contamination (flat) on " + bam1 + " and " + bam2 + " downsampling " + downsampling.toString(), spec);
}
// TODO -- Yossi will fix with JIRA GSA-765
@Test(enabled = false)
@Test
public void testHCFlatContaminationCase1() {
testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.05, "9fc24de333e8cba3f6b41ad8cc1362d8");
testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.05, "a55335e075b4ebaea31f54b88a96e829");
}
// TODO -- Yossi will fix with JIRA GSA-765
@Test(enabled = false)
@Test
public void testHCFlatContaminationCase2() {
testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.1, "57b5291ec216bf071b3c80b70f0f69bb");
testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.1, "68ea1c00e9e3f831e519a206ae7fa6b1");
}
// TODO -- Yossi will fix with JIRA GSA-765
@Test(enabled = false)
@Test
public void testHCFlatContaminationCase3() {
testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.2, "c875633954a299c9f082159b5b24aa57");
testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.2, "1e93cdc054216f0d81b0d1ae92320cfc");
}
}