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Moved the varianteval/tags/DataPoint.java and varianteval/tags/Analysis.java to varianteval/utils. This allows rsync to see these files with the -C option, as tags is some kind of reserved CVS keyword.

This commit is contained in:
Mark DePristo 2011-07-17 10:14:23 -04:00
parent 2b55d5b7c0
commit 92a1c0c278
19 changed files with 34 additions and 49 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -20,7 +20,7 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator;
@ -30,10 +30,9 @@ import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import net.sf.picard.reference.FastaSequenceFile;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import net.sf.picard.reference.ReferenceSequence;
import java.io.FileNotFoundException;
import java.io.File;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
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@ -1,12 +1,12 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
/**
* The Broad Institute

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
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@ -1,12 +1,12 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@Analysis(description = "Counts different classes of variants in the sample")

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
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@ -1,14 +1,14 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;

7
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -9,10 +10,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.phasing.AllelePair;
import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
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@ -1,11 +1,11 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
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@ -1,12 +1,12 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
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@ -1,13 +1,13 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
import org.broadinstitute.sting.utils.IndelUtils;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
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@ -1,22 +1,16 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Arrays;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* Mendelian violation detection and counting
* <p/>

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
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@ -24,12 +24,12 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
@Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites")
public class PrintMissingComp extends VariantEvaluator {

7
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -8,11 +9,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Degeneracy;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Sample;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
import java.util.ArrayList;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
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@ -1,13 +1,13 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ConcurrentMap;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
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@ -1,12 +1,12 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.utils.BaseUtils;
@Analysis(description = "Ti/Tv Variant Evaluator")

5
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
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@ -1,14 +1,13 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.*;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
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@ -25,14 +25,14 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
import org.broadinstitute.sting.utils.collections.Pair;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.tags;
package org.broadinstitute.sting.gatk.walkers.varianteval.util;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
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@ -23,8 +23,6 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.util;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.lang.annotation.Annotation;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.tags;
package org.broadinstitute.sting.gatk.walkers.varianteval.util;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
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@ -7,15 +7,12 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.StandardEval;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.RequiredStratification;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.StandardStratification;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;