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Added: integration test for extended pileup (with indels included) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2481 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-12-29 23:02:23 +00:00
parent c928347c0c
commit 4aeb50c87d
1 changed files with 11 additions and 0 deletions
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11
java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java
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@ -23,4 +23,15 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5));
executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases", spec);
}
@Test
public void testExtendedEventPileup() {
String gatk_args = "-T Pileup -I " + validationDataLocation + "OV-0930.normal.chunk.bam "
+ "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"
+ " -show_indels -o %s";
String expected_md5="afc9ef7f4668e82d0bf88ab8916944f4";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args,1,Arrays.asList(expected_md5));
executeTest("Testing the extended pileup with indel records included on a small chunk of Ovarian dataset with 20 indels (1 D, 19 I)", spec);
}
}