From 1c387848de71fc0ee66fcb9aa97f943b50d14699 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 2 Aug 2011 10:39:50 -0400 Subject: [PATCH] No more use of -D in the integration tests but instead stick with VCFs only. Since all of these tests were duplicated (one each for dbSNP format and for VCF), we don't actually lose coverage in the integration tests. --- .../indels/IndelRealignerIntegrationTest.java | 19 ------------------- .../indels/IndelRealignerPerformanceTest.java | 4 ++-- 2 files changed, 2 insertions(+), 21 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index 2676f7067..19dc99682 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -32,13 +32,6 @@ public class IndelRealignerIntegrationTest extends WalkerTest { 1, Arrays.asList(base_md5_with_SW_or_VCF)); executeTest("test realigner defaults with VCF", spec2); - - WalkerTestSpec spec3 = new WalkerTestSpec( - baseCommand + "-D " + GATKDataLocation + "dbsnp_129_b36.rod", - 1, - Arrays.asList(base_md5)); - executeTest("realigner defaults with dbsnp", spec3); - } @Test @@ -48,12 +41,6 @@ public class IndelRealignerIntegrationTest extends WalkerTest { 1, Arrays.asList("3dd5d2c9931b375455af0bff1a2c4888")); executeTest("realigner known indels only from VCF", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -D " + GATKDataLocation + "dbsnp_129_b36.rod", - 1, - Arrays.asList("05a114623c126b0398fbc1703437461e")); - executeTest("realigner known indels only from dbsnp", spec2); } @Test @@ -63,12 +50,6 @@ public class IndelRealignerIntegrationTest extends WalkerTest { 1, Arrays.asList(base_md5_with_SW_or_VCF)); executeTest("realigner use SW from VCF", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - baseCommand + "--consensusDeterminationModel USE_SW -D " + GATKDataLocation + "dbsnp_129_b36.rod", - 1, - Arrays.asList(base_md5_with_SW_or_VCF)); - executeTest("realigner use SW from dbsnp", spec2); } @Test diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java index fd5ad0b22..e8b5033cf 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java @@ -30,7 +30,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest { " -LOD 5" + " -maxConsensuses 100" + " -greedy 100" + - " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" + + " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" + " -o /dev/null" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + " -L chr1:1-5,650,000" + @@ -45,7 +45,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest { " -LOD 5" + " -maxConsensuses 100" + " -greedy 100" + - " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" + + " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" + " -o /dev/null" + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + " -L chr1:1-150,000,000" +