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Renaming and moving relevant tools into a sequenom directory 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2971 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-10 02:31:10 +00:00
parent c638c29eea
commit 6e855809e1
5 changed files with 30 additions and 4 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java → java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.walkers.fasta;
package org.broadinstitute.sting.gatk.walkers.sequenom;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

2
java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java → java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.walkers.fasta;
package org.broadinstitute.sting.gatk.walkers.sequenom;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java → java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantstovcf;
package org.broadinstitute.sting.gatk.walkers.sequenom;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -25,7 +25,7 @@ import java.util.*;
* Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes)
*/
@Reference(window=@Window(start=0,stop=40))
public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
public class SequenomValidationConverter extends RodWalker<VCFRecord,Integer> {
@Argument(fullName="outputVCF", shortName="vcf", doc="The VCF file to write results", required=true)
protected File vcfFile = null;
@Argument(fullName="maxHardy", doc="Maximum phred-scaled Hardy-Weinberg violation pvalue to consider an assay valid [default:20]", required=false)

0
java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCFIntegrationTest.java → java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PlinkToVCFIntegrationTest.java
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26
java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java 100755
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@ -0,0 +1,26 @@
package org.broadinstitute.sting.gatk.walkers.sequenom;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
public class SequenomValidationConverterIntegrationTest extends WalkerTest {
@Test
public void testSNPs() {
String testPedFile = validationDataLocation + "Sequenom_Test_File.txt";
String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B input,Plink,"+testPedFile+" -vcf %s";
WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
Arrays.asList("02dcb683db503599efed0b76daa8fcba"));
executeTest("Test SNPs", spec);
}
@Test
public void testIndels() {
String testPedFile = validationDataLocation + "pilot2_indel_validation.renamed.ped";
String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B input,Plink,"+testPedFile+" -vcf %s";
WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
Arrays.asList("e72c0ab95b279a4d39cc14d40770a801"));
executeTest("Test Indels", spec);
}
}