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Moving experimental annotations from core to oneoffs 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2528 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-01-06 19:34:10 +00:00
parent a32245f7d2
commit 7e3e714d3c
3 changed files with 12 additions and 8 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.Pair;
@ -8,6 +9,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.walkers.annotator.*;
import java.util.Map;
@ -18,7 +20,7 @@ import java.util.Map;
* Time: 2:48:15 PM
* To change this template use File | Settings | File Templates.
*/
public class ProportionOfNonrefBasesSupportingSNP implements VariantAnnotation{
public class ProportionOfNonrefBasesSupportingSNP implements VariantAnnotation {
private String KEY_NAME = "prop_nonref_that_are_snp";
public String getKeyName() { return KEY_NAME; }

7
java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Pair;
@ -18,7 +19,7 @@ import java.io.PrintWriter;
import java.io.FileOutputStream;
import java.util.List;
import java.util.Map;
import org.broadinstitute.sting.gatk.walkers.annotator.*;
/**
* Created by IntelliJ IDEA.
* User: chartl
@ -26,7 +27,7 @@ import java.util.Map;
* Time: 2:18:43 PM
* To change this template use File | Settings | File Templates.
*/
public class ProportionOfRefSecondBasesSupportingSNP implements VariantAnnotation{
public class ProportionOfRefSecondBasesSupportingSNP implements VariantAnnotation {
private String KEY_NAME = "ref_2bb_snp_prop";
private boolean USE_MAPQ0_READS = false;

7
java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java
View File

@ -1,8 +1,9 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.Pair;
@ -11,7 +12,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import java.util.Map;
import org.broadinstitute.sting.gatk.walkers.annotator.*;
/**
* Created by IntelliJ IDEA.
* User: chartl
@ -19,7 +20,7 @@ import java.util.Map;
* Time: 2:42:05 PM
* To change this template use File | Settings | File Templates.
*/
public class ProportionOfSNPSecondBasesSupportingRef implements VariantAnnotation{
public class ProportionOfSNPSecondBasesSupportingRef implements VariantAnnotation {
public String KEY_NAME = "SNP_2B_SUPPORT_REF";
public boolean USE_MAPQ0_READS = false;
public String debug_file = "/humgen/gsa-scr1/chartl/temporary/ProportionOfRefSecondBasesSupportingSNP.debug.txt";