diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java index e864e5754..5e46f8f6f 100755 --- a/public/java/test/org/broadinstitute/sting/BaseTest.java +++ b/public/java/test/org/broadinstitute/sting/BaseTest.java @@ -64,7 +64,7 @@ public abstract class BaseTest { public static final String b37Refseq = refseqAnnotationLocation + "refGene-big-table-b37.txt"; public static final String dbsnpDataLocation = GATKDataLocation; - public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf"; + public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf"; public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf"; public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/"; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 84e52f037..fc50f67f2 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -94,7 +94,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testDBTagWithDbsnp() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1, + baseTestString() + " -B:dbsnp,vcf " + b36dbSNP129 + " -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1, Arrays.asList("3da8ca2b6bdaf6e92d94a8c77a71313d")); executeTest("getting DB tag with dbSNP", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java index 6d2841d6f..be2f3cdaa 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java @@ -24,7 +24,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest { executeTest("testFastaReference", spec1b); WalkerTestSpec spec2 = new WalkerTestSpec( - "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s", + "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s", 1, Arrays.asList("0567b32ebdc26604ddf2a390de4579ac")); executeTest("testFastaAlternateReferenceIndels", spec2); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java index 738580ab1..d271d78b1 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java @@ -15,7 +15,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest { " -glm BOTH" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + " -L chr1:1-50,000,000" + - " -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + + " -B:dbsnp,VCF " + b36dbSNP129 + " -o /dev/null", 0, new ArrayList(0)); @@ -30,7 +30,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest { " -glm BOTH" + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + - " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + + " -B:dbsnp,vcf " + b36dbSNP129 + " -o /dev/null", 0, new ArrayList(0)); @@ -46,7 +46,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest { " -glm BOTH" + " -L chr1:1-50,000,000" + " -nt 10" + - " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + + " -B:dbsnp,vcf " + b36dbSNP129 + " -o /dev/null", 0, new ArrayList(0)); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java index f5ed69476..aabf01415 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java @@ -17,7 +17,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest { executeTest("test standard", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( - "-T RealignerTargetCreator -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s", + "-T RealignerTargetCreator -B:dbsnp,vcf " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s", 1, Arrays.asList("0367d39a122c8ac0899fb868a82ef728")); executeTest("test dbsnp", spec2); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java index ecef7ca90..469425dcd 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java @@ -55,7 +55,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + + " -B:dbsnp,vcf " + b36dbSNP129 + " -T CountCovariates" + " -I " + bam + ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) @@ -136,7 +136,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { " -standard" + " -OQ" + " -recalFile %s" + - " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf", + " -B:dbsnp,vcf " + b36dbSNP129, 1, // just one output file Arrays.asList(md5)); executeTest("testCountCovariatesUseOriginalQuals", spec); @@ -183,7 +183,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + + " -B:dbsnp,vcf " + b36dbSNP129 + " -T CountCovariates" + " -I " + bam + " -standard" + @@ -288,7 +288,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { " -B:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" + " -T CountCovariates" + " -I " + bam + - " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + + " -B:dbsnp,vcf " + b36dbSNP129 + " -L 1:10,000,000-10,200,000" + " -cov ReadGroupCovariate" + " -cov QualityScoreCovariate" + @@ -313,7 +313,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + + " -B:dbsnp,vcf " + " -T CountCovariates" + " -I " + bam + " -cov ReadGroupCovariate" + diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java index b6fa89303..7cdb6af95 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java @@ -15,7 +15,7 @@ public class VariantContextIntegrationTest extends WalkerTest { " -R " + b36KGReference; private static String root = cmdRoot + - " -L 1:1-1,000,000 -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + + " -L 1:1-1,000,000 -B:dbsnp,vcf " + b36dbSNP129 + " -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf"; private static final class VCITTest extends TestDataProvider {