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adding the GELI ROD validation 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3270 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-04-29 21:43:00 +00:00
parent 82818a417b
commit 7fbfd34315
2 changed files with 27 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/RodSystemValidationWalker.java → java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.validation; package org.broadinstitute.sting.playground.gatk.walkers.validation;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -22,7 +22,7 @@ import java.util.List;
public class RodSystemValidationWalker extends RodWalker<Integer,Integer> { public class RodSystemValidationWalker extends RodWalker<Integer,Integer> {
// the divider to use in some of the text output // the divider to use in some of the text output
private static final String DIVIDER = "-->"; private static final String DIVIDER = ",";
// used to calculate the MD5 of a file // used to calculate the MD5 of a file
MessageDigest digest = null; MessageDigest digest = null;

25
java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java 100644
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@ -0,0 +1,25 @@
package org.broadinstitute.sting.playground.gatk.walkers.validation;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
/**
* The pile-up tests, that test any changes to the underlying ROD system
*/
public class RodSystemValidationIntegrationTest extends WalkerTest {
public static String baseTestString() {
return "-T RodSystemValidation -o %s -R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
}
@Test
public void testSimpleGeliPileup() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B eval,Variants," + validationDataLocation + "ROD_validation/chr1.geli", 1,
Arrays.asList("536567b13ea4b8786badd96c879df245"));
executeTest("testVCFSelect1", spec);
}
}