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adding more ROD pile-up tests 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3301 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-05-05 16:01:11 +00:00
parent 0338345bee
commit ad11201235
1 changed files with 36 additions and 6 deletions
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42
java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java
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@ -10,16 +10,46 @@ import java.util.Arrays;
*/ */
public class RodSystemValidationIntegrationTest extends WalkerTest { public class RodSystemValidationIntegrationTest extends WalkerTest {
public static String baseTestString() { public static String baseTestString1KG() {
return "-T RodSystemValidation -o %s -R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"; return "-T RodSystemValidation -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta";
} }
@Test @Test
public void testSimpleGeliPileup() { public void testSimpleGeliPileup() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B eval,GeliText," + validationDataLocation + "ROD_validation/chr1.geli", 1, baseTestString1KG() + " -B eval,GeliText," + validationDataLocation + "ROD_validation/chr1.geli", 1,
Arrays.asList("0d338375f724dd2b5481a8606892c772")); Arrays.asList("832efb29a6d4e8dbae374d3eeee17d9d"));
executeTest("testVCFSelect1", spec); executeTest("testSimpleGeliPileup", spec);
}
@Test
public void testSimpleVCFPileup() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf", 1,
Arrays.asList("ff4da30a3b6428bc64d61214c715efa5"));
executeTest("testSimpleVCFPileup", spec);
}
@Test
public void testComplexVCFPileup() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf" +
" -B eval,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf"
, 1,
Arrays.asList("52f758a70ae603213d4399220151357d"));
executeTest("testComplexVCFPileup", spec);
}
@Test
public void testLargeComplexVCFPileup() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf" +
" -B eval,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf" +
" -B eval,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf" +
" -L 1 -L 2 -L 20"
, 1,
Arrays.asList("421a27be91496e88f2f4e197dcfad0ff"));
executeTest("testLargeComplexVCFPileup", spec);
} }
} }