From d89bc2c796a123353606055a624ea851047bc215 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 14 Oct 2009 17:16:36 +0000 Subject: [PATCH] This class no longer outputs in sequenom format git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1832 348d0f76-0448-11de-a6fe-93d51630548a --- .../FastaAlternateReferenceIntegrationTest.java | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java index bcb062b84..a38082192 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java @@ -21,22 +21,10 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest { Arrays.asList("3a48986c3832a768b478c3e95f994b0f")); executeTest("testFastaAlternateReferenceIndels", spec2); - WalkerTestSpec spec3 = new WalkerTestSpec( - "-T FastaAlternateReferenceMaker -sequenom -R /broad/1KG/reference/human_b36_both.fasta -B indels,PointIndel,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.indels -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -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("b53b067a3bdada202dba7d3c382ae1d0")); - executeTest("testFastaAlternateReferenceIndelSequenom", spec3); - WalkerTestSpec spec4 = new WalkerTestSpec( "-T FastaAlternateReferenceMaker -R /broad/1KG/reference/human_b36_both.fasta -B snps,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s", 1, Arrays.asList("82705a88f6fc25880dd2331183531d9a")); executeTest("testFastaAlternateReferenceSnps", spec4); - - WalkerTestSpec spec5 = new WalkerTestSpec( - "-T FastaAlternateReferenceMaker -sequenom -R /broad/1KG/reference/human_b36_both.fasta -B snps,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s", - 1, - Arrays.asList("c6744c61009a7c15899ce4ef1faa0000")); - executeTest("testFastaAlternateReferenceSnpsSequenom", spec5); } }