diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/CallsetConcordanceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/CallsetConcordanceWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java index 354a4d365..3d5041eb9 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/CallsetConcordanceWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.concordance; +package org.broadinstitute.sting.gatk.walkers.concordance; import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.refdata.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/ConcordanceType.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/ConcordanceType.java similarity index 85% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/ConcordanceType.java rename to java/src/org/broadinstitute/sting/gatk/walkers/concordance/ConcordanceType.java index 7b97c647d..9e7340ae9 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/ConcordanceType.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/ConcordanceType.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.concordance; +package org.broadinstitute.sting.gatk.walkers.concordance; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeCall; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/IndelSubsets.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/IndelSubsets.java rename to java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java index 0778145ab..c3ee233d7 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/IndelSubsets.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.concordance; +package org.broadinstitute.sting.gatk.walkers.concordance; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/NWayVenn.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/NWayVenn.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/NWayVenn.java rename to java/src/org/broadinstitute/sting/gatk/walkers/concordance/NWayVenn.java index 8ad32ad52..778a9a952 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/NWayVenn.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/NWayVenn.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.concordance; +package org.broadinstitute.sting.gatk.walkers.concordance; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeCall; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java rename to java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java index e38b82c0f..4cb68dfb9 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.concordance; +package org.broadinstitute.sting.gatk.walkers.concordance; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.StingException; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java rename to java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java index 4761fd825..43e22840c 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.concordance; +package org.broadinstitute.sting.gatk.walkers.concordance; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.genotype.Variation; diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java new file mode 100755 index 000000000..ca0db4d25 --- /dev/null +++ b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java @@ -0,0 +1,36 @@ +package org.broadinstitute.sting.gatk.walkers.concordance; + +import org.broadinstitute.sting.WalkerTest; +import org.junit.Test; + +import java.util.Arrays; + +public class CallsetConcordanceIntegrationTest extends WalkerTest { + public static String baseTestString() { + return "-T CallsetConcordance -R /broad/1KG/reference/human_b36_both.fasta -L 1:1-8000 -CO %s"; + } + + @Test + public void testSimpleVenn() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -CT SimpleVenn", 1, + Arrays.asList("0a71c8f06b4179ba59cefad962cd034c")); + executeTest("testSimpleVenn", spec); + } + + @Test + public void testSNPConcordance() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -CT SNPGenotypeConcordance:qscore=5", 1, + Arrays.asList("5da8bf664813f0ab8b22070097f6900e")); + executeTest("testSNPConcordance", spec); + } + + @Test + public void testNWayVenn() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -B set3,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/CEU.sample.vcf -CT NWayVenn", 1, + Arrays.asList("9da88442eea094da8b6110d8f5ed4408")); + executeTest("testNWayVenn", spec); + } +} \ No newline at end of file