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almost managed to move things around perfectly in move go 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2788 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-02-05 14:18:26 +00:00
parent 9e5c18d50f
commit c6d86da4b8
18 changed files with 29 additions and 46 deletions
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2
java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Allele.java → java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Allele.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext; package org.broadinstitute.sting.gatk.contexts.variantcontext;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;

6
java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Genotype.java → java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Genotype.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext; package org.broadinstitute.sting.gatk.contexts.variantcontext;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.StingException;
import java.util.*; import java.util.*;
@ -12,6 +11,7 @@ import java.util.*;
*/ */
public class Genotype { public class Genotype {
protected InferredGeneticContext commonInfo; protected InferredGeneticContext commonInfo;
public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
protected List<Allele> alleles = new ArrayList<Allele>(); protected List<Allele> alleles = new ArrayList<Allele>();
public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes) { public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
@ -25,7 +25,7 @@ public class Genotype {
} }
public Genotype(String sampleName, List<Allele> alleles) { public Genotype(String sampleName, List<Allele> alleles) {
this(sampleName, alleles, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null); this(sampleName, alleles, NO_NEG_LOG_10PERROR, null, null);
} }

3
java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/InferredGeneticContext.java → java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/InferredGeneticContext.java
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@ -1,6 +1,5 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext; package org.broadinstitute.sting.gatk.contexts.variantcontext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import java.util.*; import java.util.*;

4
java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableGenotype.java → java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/MutableGenotype.java
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@ -1,6 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext; package org.broadinstitute.sting.gatk.contexts.variantcontext;
import org.broadinstitute.sting.utils.Utils;
import java.util.*; import java.util.*;

3
java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableVariantContext.java → java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/MutableVariantContext.java
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@ -1,8 +1,7 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext; package org.broadinstitute.sting.gatk.contexts.variantcontext;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.BaseUtils;
import java.util.*; import java.util.*;

3
java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContext.java → java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContext.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext; package org.broadinstitute.sting.gatk.contexts.variantcontext;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
@ -160,6 +160,7 @@ import java.util.*;
*/ */
public class VariantContext { public class VariantContext {
protected InferredGeneticContext commonInfo = null; protected InferredGeneticContext commonInfo = null;
public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
/** The location of this VariantContext */ /** The location of this VariantContext */
private GenomeLoc loc; private GenomeLoc loc;

3
java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextUtils.java → java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -1,11 +1,10 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext; package org.broadinstitute.sting.gatk.contexts.variantcontext;
import java.util.*; import java.util.*;
import org.apache.commons.jexl.*; import org.apache.commons.jexl.*;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
public class VariantContextUtils { public class VariantContextUtils {
/** /**
* A simple but common wrapper for matching VariantContext objects using JEXL expressions * A simple but common wrapper for matching VariantContext objects using JEXL expressions

9
java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextAdaptors.java → java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -1,10 +1,11 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext; package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord; import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeEncoding; import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeEncoding;
import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord; import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
import java.util.*; import java.util.*;
@ -143,7 +144,7 @@ public class VariantContextAdaptors {
for ( VCFGenotypeEncoding s : vcfG.getAlleles() ) for ( VCFGenotypeEncoding s : vcfG.getAlleles() )
genotypeAlleles.add(Allele.getMatchingAllele(alleles, s.getBases())); genotypeAlleles.add(Allele.getMatchingAllele(alleles, s.getBases()));
double pError = vcfG.getNegLog10PError() == VCFGenotypeRecord.MISSING_GENOTYPE_QUALITY ? InferredGeneticContext.NO_NEG_LOG_10PERROR : vcfG.getNegLog10PError(); double pError = vcfG.getNegLog10PError() == VCFGenotypeRecord.MISSING_GENOTYPE_QUALITY ? Genotype.NO_NEG_LOG_10PERROR : vcfG.getNegLog10PError();
Map<String, String> fields = new HashMap<String, String>(); Map<String, String> fields = new HashMap<String, String>();
for ( Map.Entry<String, String> e : vcfG.getFields().entrySet() ) { for ( Map.Entry<String, String> e : vcfG.getFields().entrySet() ) {

2
java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/TestVariantContextWalker.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext; package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java
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@ -3,8 +3,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.oneoffprojects.variantcontext.Genotype; import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import java.util.List; import java.util.List;

8
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java
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@ -3,12 +3,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
import org.broadinstitute.sting.oneoffprojects.variantcontext.Genotype;
import org.broadinstitute.sting.oneoffprojects.variantcontext.Allele;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;

7
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java
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@ -3,14 +3,13 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.oneoffprojects.variantcontext.Genotype; import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
import org.broadinstitute.sting.oneoffprojects.variantcontext.Allele; import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import java.util.List; import java.util.List;
import java.util.Arrays; import java.util.Arrays;
import java.util.ArrayList;
import java.util.regex.Pattern; import java.util.regex.Pattern;
import java.util.regex.Matcher; import java.util.regex.Matcher;

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java
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@ -3,9 +3,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.oneoffprojects.variantcontext.Genotype;
import org.broadinstitute.sting.utils.StingException;
import java.util.List; import java.util.List;
import java.util.Arrays; import java.util.Arrays;

5
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
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@ -2,14 +2,13 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContextAdaptors;
import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContextUtils;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import java.util.*; import java.util.*;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java
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@ -1,9 +1,9 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2; package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import java.util.List; import java.util.List;
import java.util.ArrayList; import java.util.ArrayList;

10
java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java
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@ -1,19 +1,13 @@
package org.broadinstitute.sting.playground.gatk.walkers.diagnostics; package org.broadinstitute.sting.playground.gatk.walkers.diagnostics;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.RODRecordList;
import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContextAdaptors;
import java.util.*;
/** /**
* Computes the density of SNPs passing and failing filters in intervals on the genome and emits a table for display * Computes the density of SNPs passing and failing filters in intervals on the genome and emits a table for display

0
java/test/org/broadinstitute/sting/oneoffprojects/variantcontext/AlleleTest.java → java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/variantcontext/AlleleTest.java
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0
java/test/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextTest.java → java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/variantcontext/VariantContextTest.java
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