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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
This commit is contained in:
chartl 2010-01-21 17:35:20 +00:00
parent 74779a9a78
commit 5b2a1e483e
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCF.java → java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java
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@ -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<VCFRecord,Integer> {
public class PlinkToVCF extends RefWalker<VCFRecord,Integer> {
@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)

2
java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCFIntegrationTest.java
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@ -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<File> result = executeTest("TestSequenomToVCFNoSmartHardy",spec).getFirst();
}