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Integration test for GenomicAnnotator 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3167 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-04-14 14:43:25 +00:00
parent c0f4695902
commit b930dc52a5
1 changed files with 42 additions and 0 deletions
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42
java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java 100755
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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);
}
}