diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/RodSystemValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java similarity index 97% rename from java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/RodSystemValidationWalker.java rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java index b1a57266e..76a3e0a48 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/RodSystemValidationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java @@ -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.contexts.AlignmentContext; @@ -22,7 +22,7 @@ import java.util.List; public class RodSystemValidationWalker extends RodWalker { // 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 MessageDigest digest = null; diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java new file mode 100644 index 000000000..c3dc1370e --- /dev/null +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java @@ -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); + } +}