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Recent changes to the build system make the build system complain loudly about 

pieces of core that depend on playground.  Most of these have been eliminated by
(temporarily) promoting Aaron's report system to core in this checkin.  I'll 
follow up with other changes in separately.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4350 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-09-24 22:09:12 +00:00
parent 6ebca5d219
commit 497bcbcbb7
40 changed files with 80 additions and 80 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReport.java → java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.GATKReport;
package org.broadinstitute.sting.gatk.report;
import java.io.PrintStream;
import java.util.TreeMap;

2
java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReportColumn.java → java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.GATKReport;
package org.broadinstitute.sting.gatk.report;
import java.util.TreeMap;

2
java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReportTable.java → java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.GATKReport;
package org.broadinstitute.sting.gatk.report;
import java.io.PrintStream;
import java.util.HashMap;

4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CompOverlap.java
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@ -5,8 +5,8 @@ import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
/**
* The Broad Institute

4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountFunctionalClasses.java
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@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;

4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java
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@ -5,8 +5,8 @@ import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

6
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -5,9 +5,9 @@ import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.exceptions.UserException;

6
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
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@ -5,9 +5,9 @@ import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.playground.gatk.walkers.phasing.*;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.MathUtils;

6
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java
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@ -4,9 +4,9 @@ import org.broad.tribble.util.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.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
/**

4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java
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@ -6,8 +6,8 @@ import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.List;

6
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
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@ -5,9 +5,9 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList;

4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ThetaVariantEvaluator.java
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@ -6,8 +6,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.Allele;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import java.util.concurrent.ConcurrentMap;
import java.util.concurrent.ConcurrentHashMap;

4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java
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@ -5,8 +5,8 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
@Analysis(name = "Ti/Tv Variant Evaluator", description = "Ti/Tv Variant Evaluator")
public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval {

8
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -41,10 +41,10 @@ import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.variantrecalibration.ApplyVariantCuts;
import org.broadinstitute.sting.playground.utils.report.ReportMarshaller;
import org.broadinstitute.sting.playground.utils.report.VE2ReportFactory;
import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.report.ReportMarshaller;
import org.broadinstitute.sting.utils.report.VE2ReportFactory;
import org.broadinstitute.sting.utils.report.templates.ReportFormat;
import org.broadinstitute.sting.utils.report.utils.Node;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.classloader.PackageUtils;
import org.broadinstitute.sting.utils.Utils;

6
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java
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@ -31,9 +31,9 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.collections.Pair;
import java.util.ArrayList;

6
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java
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@ -5,9 +5,9 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.analysis.AminoAcid;
import org.broadinstitute.sting.utils.analysis.AminoAcidTable;
import org.broadinstitute.sting.utils.analysis.AminoAcidUtils;

6
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java
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@ -6,11 +6,11 @@ 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.VariantEvaluatorBySample;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.SampleDataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluatorBySample;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import java.util.ArrayList;
import java.util.List;

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java
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@ -8,8 +8,8 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.SampleDataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluatorBySample;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import java.util.ArrayList;
import java.util.List;

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java
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@ -5,8 +5,8 @@ import org.broad.tribble.util.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.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType;
import java.util.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ErrorRatePerCycle.java
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@ -8,7 +8,7 @@ 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.LocusWalker;
import org.broadinstitute.sting.playground.utils.report.GATKReport.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.utils.BaseUtils;
import java.io.PrintStream;

8
java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java → java/src/org/broadinstitute/sting/utils/report/AnalysisModuleScanner.java
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@ -21,11 +21,11 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report;
package org.broadinstitute.sting.utils.report;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.tags.Param;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.tags.Param;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.lang.annotation.Annotation;

8
java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java → java/src/org/broadinstitute/sting/utils/report/ReportMarshaller.java
View File

@ -21,12 +21,12 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report;
package org.broadinstitute.sting.utils.report;
import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat;
import org.broadinstitute.sting.playground.utils.report.utils.ComplexDataUtils;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.report.templates.ReportFormat;
import org.broadinstitute.sting.utils.report.utils.ComplexDataUtils;
import org.broadinstitute.sting.utils.report.utils.Node;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.*;

6
java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java → java/src/org/broadinstitute/sting/utils/report/VE2ReportFactory.java
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@ -1,7 +1,7 @@
package org.broadinstitute.sting.playground.utils.report;
package org.broadinstitute.sting.utils.report;
import org.broadinstitute.sting.playground.utils.report.templates.*;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.report.templates.*;
import org.broadinstitute.sting.utils.report.utils.Node;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import java.io.*;

2
java/src/org/broadinstitute/sting/playground/utils/report/tags/Analysis.java → java/src/org/broadinstitute/sting/utils/report/tags/Analysis.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.tags;
package org.broadinstitute.sting.utils.report.tags;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;

2
java/src/org/broadinstitute/sting/playground/utils/report/tags/DataPoint.java → java/src/org/broadinstitute/sting/utils/report/tags/DataPoint.java
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@ -21,7 +21,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report.tags;
package org.broadinstitute.sting.utils.report.tags;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;

2
java/src/org/broadinstitute/sting/playground/utils/report/tags/Param.java → java/src/org/broadinstitute/sting/utils/report/tags/Param.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.tags;
package org.broadinstitute.sting.utils.report.tags;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;

2
java/src/org/broadinstitute/sting/playground/utils/report/templates/CSVFormat.java → java/src/org/broadinstitute/sting/utils/report/templates/CSVFormat.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.templates;
package org.broadinstitute.sting.utils.report.templates;
/**
* the basic comma separated value format

4
java/src/org/broadinstitute/sting/playground/utils/report/templates/GrepFormat.java → java/src/org/broadinstitute/sting/utils/report/templates/GrepFormat.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.playground.utils.report.templates;
package org.broadinstitute.sting.utils.report.templates;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.report.utils.Node;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;

4
java/src/org/broadinstitute/sting/playground/utils/report/templates/RFormat.java → java/src/org/broadinstitute/sting/utils/report/templates/RFormat.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.playground.utils.report.templates;
package org.broadinstitute.sting.utils.report.templates;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.report.utils.Node;
import java.io.PrintWriter;
import java.io.Writer;

4
java/src/org/broadinstitute/sting/playground/utils/report/templates/ReportFormat.java → java/src/org/broadinstitute/sting/utils/report/templates/ReportFormat.java
View File

@ -1,6 +1,6 @@
package org.broadinstitute.sting.playground.utils.report.templates;
package org.broadinstitute.sting.utils.report.templates;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.report.utils.Node;
import java.io.File;
import java.io.Writer;

4
java/src/org/broadinstitute/sting/playground/utils/report/templates/TableBasedFormat.java → java/src/org/broadinstitute/sting/utils/report/templates/TableBasedFormat.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.playground.utils.report.templates;
package org.broadinstitute.sting.utils.report.templates;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.report.utils.Node;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.*;

2
java/src/org/broadinstitute/sting/playground/utils/report/templates/TableFormat.java → java/src/org/broadinstitute/sting/utils/report/templates/TableFormat.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report.templates;
package org.broadinstitute.sting.utils.report.templates;
/**

2
java/src/org/broadinstitute/sting/playground/utils/report/templates/TextTable.java → java/src/org/broadinstitute/sting/utils/report/templates/TextTable.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.templates;
package org.broadinstitute.sting.utils.report.templates;
import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/playground/utils/report/utils/ComplexDataUtils.java → java/src/org/broadinstitute/sting/utils/report/utils/ComplexDataUtils.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.utils;
package org.broadinstitute.sting.utils.report.utils;
import java.util.*;

2
java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java → java/src/org/broadinstitute/sting/utils/report/utils/Node.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.utils;
package org.broadinstitute.sting.utils.report.utils;
import java.util.*;

2
java/src/org/broadinstitute/sting/playground/utils/report/utils/NodeUtils.java → java/src/org/broadinstitute/sting/utils/report/utils/NodeUtils.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.utils;
package org.broadinstitute.sting.utils.report.utils;
import java.util.ArrayList;
import java.util.List;

2
java/src/org/broadinstitute/sting/playground/utils/report/utils/TableType.java → java/src/org/broadinstitute/sting/utils/report/utils/TableType.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.utils;
package org.broadinstitute.sting.utils.report.utils;
/**

8
java/test/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScannerUnitTest.java → java/test/org/broadinstitute/sting/utils/report/AnalysisModuleScannerUnitTest.java
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@ -1,9 +1,9 @@
package org.broadinstitute.sting.playground.utils.report;
package org.broadinstitute.sting.utils.report;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.tags.Param;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.tags.Param;
import org.junit.Assert;
import org.junit.Test;

2
java/test/org/broadinstitute/sting/playground/utils/report/ReportMarshallerUnitTest.java → java/test/org/broadinstitute/sting/utils/report/ReportMarshallerUnitTest.java
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@ -21,7 +21,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report;
package org.broadinstitute.sting.utils.report;
import org.broadinstitute.sting.BaseTest;
import org.junit.Test;

2
java/test/org/broadinstitute/sting/playground/utils/report/templates/TextTableUnitTest.java → java/test/org/broadinstitute/sting/utils/report/templates/TextTableUnitTest.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.utils.report.templates;
package org.broadinstitute.sting.utils.report.templates;
import org.junit.Assert;
import org.junit.Test;