zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java
View File

@ -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.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.Pair; 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.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.walkers.annotator.*;
import java.util.Map; import java.util.Map;

5
java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java
View File

@ -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.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.Pair;
@ -18,7 +19,7 @@ import java.io.PrintWriter;
import java.io.FileOutputStream; import java.io.FileOutputStream;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import org.broadinstitute.sting.gatk.walkers.annotator.*;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
* User: chartl * User: chartl

5
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.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; 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.Variation;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.Pair; 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 org.broadinstitute.sting.utils.pileup.PileupElement;
import java.util.Map; import java.util.Map;
import org.broadinstitute.sting.gatk.walkers.annotator.*;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
* User: chartl * User: chartl