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Added test of Nway cleaning for Matt; thanks to Aaron for the help. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2977 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-10 21:00:41 +00:00
parent 486bef9318
commit 40d305bc7e
1 changed files with 17 additions and 2 deletions
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19
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
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@ -4,6 +4,7 @@ import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
import java.io.File;
public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
@ -14,13 +15,27 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
"-T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023800-10332350 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -snps %s",
2,
Arrays.asList(md5lod5));
executeTest("testLod5", spec1);
executeTest("test Lod5", spec1);
String[] md5lod200 = {"96edef86cea95f312ee8295b38227eb8", "d4d8ff567b614729ab8c52bd7d6bef48"};
WalkerTestSpec spec2 = new WalkerTestSpec(
"-T IndelRealigner -LOD 200 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023800-10332350 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -snps %s",
2,
Arrays.asList(md5lod200));
executeTest("testLod200", spec2);
executeTest("test Lod200", spec2);
String filename1 = "NA12878.chrom1.SLX.SRP000032.2009_06";
String filename2 = "low_coverage_CEU.chr1.10k-11k";
WalkerTestSpec spec3 = new WalkerTestSpec(
"-T IndelRealigner -nway -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + filename1 + ".bam -I " + validationDataLocation + filename2 + ".bam -L 1:10023900-10024000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O /tmp -snps %s",
1,
Arrays.asList("bd42a4fa66d7ec7a480c2b94313a78d3"));
File file1 = new File("/tmp/" + filename1 + ".cleaned.bam");
file1.deleteOnExit();
spec3.addAuxFile("7e1c5a74e572c3e0fbc14f98021e04b4", file1);
File file2 = new File("/tmp/" + filename2 + ".cleaned.bam");
file2.deleteOnExit();
spec3.addAuxFile("7a796195c3f13a3c84cd7209f3030d85", file2);
executeTest("test NWay", spec3);
}
}