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Adding cleaner test 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1561 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-09 16:05:56 +00:00
parent 9c7f456510
commit bed646e4f6
1 changed files with 33 additions and 0 deletions
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33
java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java 100755
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package org.broadinstitute.sting.gatk.walkers.indels;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
public class IntervalCleanerIntegrationTest extends WalkerTest {
@Test
public void testIntervals() {
String[] md5lod5 = {"bfe1c76bf352b22f79c9b7242197a126", "4aa3637e86822c95af3e2c9b414530c3"};
WalkerTestSpec spec1 = new WalkerTestSpec(
"-T IntervalCleaner -stats blah1.stats -LOD 5 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
2,
Arrays.asList(md5lod5));
executeTest("testLod5", spec1);
String[] md5lod200 = {"4481e4d24d61a3e438323b368ad0eee7", "e39aa718c9810364ebe30964d878d5ff"};
WalkerTestSpec spec2 = new WalkerTestSpec(
"-T IntervalCleaner -LOD 200 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
2,
Arrays.asList(md5lod200));
executeTest("testLod200", spec2);
String[] md5cleanedOnly = {"c8da42cc2298e05ab4f2bc9e5d7445e1", "4aa3637e86822c95af3e2c9b414530c3"};
WalkerTestSpec spec3 = new WalkerTestSpec(
"-T IntervalCleaner -LOD 5 -cleanedOnly -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
2,
Arrays.asList(md5cleanedOnly));
executeTest("testCleanedOnly", spec3);
}
}