diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index 15d808ebe..c9c5e09a8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java index 76db330ed..85373baa8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java @@ -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 diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java index c4277adc9..befb2ff13 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java @@ -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") diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java index 4b56cf130..58803c9d0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java index 3d14dd0e5..407b71893 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java index 5daf33a9f..f7f9fce0c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java index eca6c5193..dd4bb492e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java index 48b06d532..1bd420e0a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index 85e0b5889..16ec74433 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -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 *

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java index 7d54d0df8..e83914ef8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java @@ -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 { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java index deed05508..395309975 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index 89c67cfe9..f9cda5e0b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index 8811dc001..deeafd851 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -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") diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java index 405f35635..756427581 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java @@ -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.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java index 4af14810b..29a61e27a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java similarity index 80% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java index 129d5a95d..2b37ce210 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java index c8d917040..db44e9e28 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java similarity index 77% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java index 3ba448049..396843252 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index b8e45e462..eabd2e588 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -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;