diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java new file mode 100755 index 000000000..1f0d6237b --- /dev/null +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java @@ -0,0 +1,42 @@ +package org.broadinstitute.sting.playground.gatk.walkers.annotator; + + +import java.util.Arrays; + +import org.broadinstitute.sting.WalkerTest; +import org.junit.Test; + +public class GenomicAnnotatorIntegrationTest extends WalkerTest { + @Test + public void testGenomicAnnotatorOnDbSNP() { + + /* + TODO put this test back in once it gets faster. + String[] md5 = {"d19d6d1eb52fb09e7493653dc645d92a"}; + WalkerTestSpec spec = new WalkerTestSpec( + "-T GenomicAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta " + + "-B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " + + "-B dbsnp,AnnotatorInputTable,/humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt " + + "-m " + //generate many records from one input record if necessary + "-vcf %s " + + "-BTI variant", + 1, + Arrays.asList(md5)); + executeTest("test with dbSNP", spec); + */ + + + String[] md5WithDashSArg = {"abacb974e89f8456d4168ac3b704cd4b"}; + WalkerTestSpec specWithSArg = new WalkerTestSpec( + "-T GenomicAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta " + + "-B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " + + "-B dbsnp,AnnotatorInputTable,/humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt " + + "-m " + //generate many records from one input record if necessary + "-vcf %s " + + "-BTI variant " + + "-s dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet", + 1, + Arrays.asList(md5WithDashSArg)); + executeTest("test with dbSNP and -s arg", specWithSArg); + } +} \ No newline at end of file