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Moving stuff around. ( core;playground ) ----> ( oneoffs ). I've been a bad boy, sullying the core codebase. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2745 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-01-29 22:50:03 +00:00
parent 16da5011c0
commit 97f60dbc4b
6 changed files with 11 additions and 10 deletions
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3
java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.refdata; package org.broadinstitute.sting.gatk.refdata;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.oneoffprojects.refdata.HapmapVCFROD;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
@ -77,7 +78,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
addModule("GLF", RodGLF.class); addModule("GLF", RodGLF.class);
addModule("VCF", RodVCF.class); addModule("VCF", RodVCF.class);
addModule("PicardDbSNP", rodPicardDbSNP.class); addModule("PicardDbSNP", rodPicardDbSNP.class);
addModule("HapmapVCF",HapmapVCFROD.class); addModule("HapmapVCF", HapmapVCFROD.class);
} }

10
java/src/org/broadinstitute/sting/gatk/refdata/HapmapVCFROD.java → java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java
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@ -1,5 +1,8 @@
package org.broadinstitute.sting.gatk.refdata; package org.broadinstitute.sting.oneoffprojects.refdata;
import org.broadinstitute.sting.gatk.refdata.BasicReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.gatk.refdata.VariationRod;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype; import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
@ -12,16 +15,13 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
import java.io.File; import java.io.File;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
/** /*
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
* User: chartl * User: chartl
* Date: Jan 29, 2010 * Date: Jan 29, 2010
* Time: 8:57:54 AM
* To change this template use File | Settings | File Templates.
*/ */
public class HapmapVCFROD extends BasicReferenceOrderedDatum implements VariationRod, VariantBackedByGenotype, Iterator<HapmapVCFROD> { public class HapmapVCFROD extends BasicReferenceOrderedDatum implements VariationRod, VariantBackedByGenotype, Iterator<HapmapVCFROD> {
// This is a (hopefully temporary) wrapper class for certain VCF files that we want to protect from // This is a (hopefully temporary) wrapper class for certain VCF files that we want to protect from

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/LocusConcordanceInfo.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/LocusConcordanceInfo.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample; package org.broadinstitute.sting.oneoffprojects.walkers.varianteval.multisample;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceSet.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceSet.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample; package org.broadinstitute.sting.oneoffprojects.walkers.varianteval.multisample;
import java.util.HashSet; import java.util.HashSet;
import java.util.Set; import java.util.Set;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample; package org.broadinstitute.sting.oneoffprojects.walkers.varianteval.multisample;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/VCFConcordanceCalculator.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/VCFConcordanceCalculator.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample; package org.broadinstitute.sting.oneoffprojects.walkers.varianteval.multisample;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord; import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;