From 5b2a1e483ebc3e481d2d6d596e6c6f2635d83145 Mon Sep 17 00:00:00 2001 From: chartl Date: Thu, 21 Jan 2010 17:35:20 +0000 Subject: [PATCH] Renamed SequenomToVCF as PlinkToVCF. Wiki will be changed accordingly. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2649 348d0f76-0448-11de-a6fe-93d51630548a --- .../variantstovcf/{SequenomToVCF.java => PlinkToVCF.java} | 2 +- .../walkers/variantstovcf/SequenomToVCFIntegrationTest.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/{SequenomToVCF.java => PlinkToVCF.java} (99%) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCF.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCF.java rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java index 39c5ca1e1..b170a89ec 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCF.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java @@ -21,7 +21,7 @@ import java.util.*; /** * Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes) */ -public class SequenomToVCF extends RefWalker { +public class PlinkToVCF extends RefWalker { @Argument(fullName="sequenomePedFile", shortName="sPed", doc="The sequenome file from which to generate a VCF", required=true) public File seqFile = null; @Argument(fullName="outputVCF", shortName="vcf", doc="The VCF file to write to", required=true) diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCFIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCFIntegrationTest.java index 741b41b10..fe01586e8 100644 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCFIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCFIntegrationTest.java @@ -20,7 +20,7 @@ public class SequenomToVCFIntegrationTest extends WalkerTest { String testMD5 = "a16ce402ce4492c8c0552073c0a8bdf5"; String testPedFile = "/humgen/gsa-hpprojects/GATK/data/Validation_Data/Sequenom_Test_File.txt"; String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -L 1:1000000-2000000 "+ - "-T SequenomToVCF -b36contig -ns 10 -sPed "+testPedFile+" -vcf %s"; + "-T PlinkToVCF -b36contig -ns 10 -sPed "+testPedFile+" -vcf %s"; WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs,1, Arrays.asList(testMD5)); List result = executeTest("TestSequenomToVCFNoSmartHardy",spec).getFirst(); }