diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/GenotypeWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/GenotypeWriterStorage.java
index 52c58d99f..a0351a81e 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/GenotypeWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/GenotypeWriterStorage.java
@@ -29,10 +29,10 @@ import java.io.*;
import java.util.Set;
import java.util.HashSet;
+import org.broad.tribble.vcf.VCFHeaderLine;
import org.broadinstitute.sting.gatk.io.stubs.GenotypeWriterStub;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.genotype.*;
-import org.broadinstitute.sting.utils.genotype.vcf.*;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFGenotypeWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFGenotypeWriterStorage.java
index 27150e5de..d142a5ffb 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFGenotypeWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFGenotypeWriterStorage.java
@@ -1,10 +1,10 @@
package org.broadinstitute.sting.gatk.io.storage;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
import org.broadinstitute.sting.gatk.io.stubs.GenotypeWriterStub;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
import java.io.File;
import java.util.Set;
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java
index fa03cc340..a8f69e9ed 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java
@@ -1,9 +1,9 @@
package org.broadinstitute.sting.gatk.io.stubs;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import java.io.File;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
deleted file mode 100755
index b0c5fbc01..000000000
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
+++ /dev/null
@@ -1,351 +0,0 @@
-package org.broadinstitute.sting.gatk.refdata;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.genotype.vcf.*;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.*;
-
-
-/**
- * @author aaron
- *
- * Class RodVCF
- *
- * An implementation of the ROD for VCF.
- */
-public class RodVCF extends BasicReferenceOrderedDatum implements Iterator {
- public VCFReader getReader() {
- return mReader;
- }
-
- // our VCF related information
- private VCFReader mReader;
-
- public VCFRecord getRecord() {
- return mCurrentRecord;
- }
-
- public VCFRecord mCurrentRecord;
-
- public RodVCF(String name) {
- super(name);
- }
-
- public RodVCF(String name, VCFRecord currentRecord, VCFReader reader) {
- super(name);
- mCurrentRecord = currentRecord;
- mReader = reader;
- }
-
- public void assertNotNull() {
- if ( mCurrentRecord == null ) {
- throw new UnsupportedOperationException("The current Record is null");
- }
- }
-
- @Override
- public boolean parseLine(Object header, String[] parts) throws IOException {
- throw new UnsupportedOperationException("RodVCF does not support the parseLine method");
- }
-
- public Object initialize(final File source) throws FileNotFoundException {
- if ( mReader == null ) {
- mReader = new VCFReader(source);
- }
- return mReader.getHeader();
- }
-
- @Override
- public String toString() {
- return (mCurrentRecord != null ? mCurrentRecord.toStringEncoding(mReader.getHeader()) : "");
- }
-
- public static RodVCF createIterator(String name, File file) {
- RodVCF vcf = new RodVCF(name);
- try {
- vcf.initialize(file);
- } catch (FileNotFoundException e) {
- throw new StingException("Unable to find file " + file);
- }
- return vcf;
- }
-
- public boolean hasNonRefAlleleFrequency() {
- assertNotNull();
- return mCurrentRecord.getNonRefAlleleFrequency() > 0.0;
- }
-
- /**
- * get the frequency of this variant
- *
- * @return VariantFrequency with the stored frequency
- */
- public double getNonRefAlleleFrequency() {
- assertNotNull();
- return mCurrentRecord.getNonRefAlleleFrequency();
- }
-
- public String getID() {
- assertNotNull();
- return mCurrentRecord.getID();
- }
-
- /**
- * are we a SNP? If not we're a Indel/deletion
- *
- * @return true if we're a SNP
- */
- public boolean isSNP() {
- assertNotNull();
- return mCurrentRecord.isSNP();
- }
-
- /**
- * are we a novel site? Is there a DBSNP identifier
- * or a hapmap entry for the site?
- *
- * @return true if this site is novel
- */
- public boolean isNovel() {
- assertNotNull();
- return mCurrentRecord.isNovel();
- }
-
- /**
- * are we an insertion?
- *
- * @return true if we are, false otherwise
- */
- public boolean isInsertion() {
- assertNotNull();
- return mCurrentRecord.isInsertion();
- }
-
- /**
- * are we an insertion?
- *
- * @return true if we are, false otherwise
- */
- public boolean isDeletion() {
- assertNotNull();
- return mCurrentRecord.isDeletion();
- }
-
- @Override
- public GenomeLoc getLocation() {
- assertNotNull();
- return mCurrentRecord.getLocation();
- }
-
- /**
- * get the reference base(s) at this position
- *
- * @return the reference base or bases, as a string
- */
- public String getReference() {
- assertNotNull();
- return mCurrentRecord.getReference();
- }
-
- /** are we bi-allelic?
- * @return true if we're bi-allelic
- */
- public boolean isBiallelic() {
- assertNotNull();
- return mCurrentRecord.isBiallelic();
- }
-
- /**
- * get the -1 * (log 10 of the error value)
- *
- * @return the log based error estimate
- */
- public double getNegLog10PError() {
- assertNotNull();
- return mCurrentRecord.getNegLog10PError();
- }
-
- public double getQual() {
- assertNotNull();
- return mCurrentRecord.getQual();
- }
-
- public boolean hasAlternateAllele() {
- assertNotNull();
- return mCurrentRecord.hasAlternateAllele();
- }
-
- /**
- * gets the alternate alleles. This method should return all the alleles present at the location,
- * NOT including the reference base. This is returned as a string list with no guarantee ordering
- * of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest
- * frequency).
- *
- * @return an alternate allele list
- */
- public List getAlternateAlleleList() {
- assertNotNull();
- return mCurrentRecord.getAlternateAlleleList();
- }
-
- /**
- * gets the alleles. This method should return all the alleles present at the location,
- * including the reference base. The first allele should always be the reference allele, followed
- * by an unordered list of alternate alleles.
- *
- * @return an alternate allele list
- */
- public List getAlleleList() {
- assertNotNull();
- return mCurrentRecord.getAlleleList();
- }
-
- /**
- * are we truely a variant, given a reference
- *
- * @return false if we're a variant(indel, delete, SNP, etc), true if we're not
- */
- public boolean isReference() {
- assertNotNull();
- return mCurrentRecord.isReference();
- }
-
- /**
- * are we an insertion or a deletion? yes, then return true. No? Well, false then.
- *
- * @return true if we're an insertion or deletion
- */
- public boolean isIndel() {
- assertNotNull();
- return mCurrentRecord.isIndel();
- }
-
- /**
- * gets the alternate base is the case of a SNP. Throws an IllegalStateException if we're not a SNP
- * of
- *
- * @return a char, representing the alternate base
- */
- public char getAlternativeBaseForSNP() {
- assertNotNull();
- return mCurrentRecord.getAlternativeBaseForSNP();
- }
-
- /**
- * gets the reference base is the case of a SNP. Throws an IllegalStateException if we're not a SNP
- *
- * @return a char, representing the alternate base
- */
- public char getReferenceForSNP() {
- assertNotNull();
- return mCurrentRecord.getReferenceForSNP();
- }
-
- public boolean hasGenotypeData() {
- assertNotNull();
- return mCurrentRecord.hasGenotypeData();
- }
-
- /**
- * get the genotypes
- *
- * @return a list of the genotypes
- */
- public List getVCFGenotypeRecords() {
- assertNotNull();
- return mCurrentRecord.getVCFGenotypeRecords();
- }
-
- /**
- * Returns the genotype associated with sample, or null if the genotype is missing
- *
- * @param sampleName the name of the sample genotype to fetch
- * @return genotype record
- */
- public VCFGenotypeRecord getGenotype(final String sampleName) {
- return mCurrentRecord.getGenotype(sampleName);
- }
-
- public String[] getSampleNames() {
- assertNotNull();
- return mCurrentRecord.getSampleNames();
- }
-
-// public Map getSampleGenotypes() {
-// String[] samples = getSampleNames();
-// List genotypes = getGenotypes();
-// HashMap map = new HashMap();
-//
-// for ( int i = 0; i < samples.length; i++ ) {
-// map.put(samples[i], genotypes.get(i));
-// }
-//
-// return map;
-// }
-
- public Map getInfoValues() {
- assertNotNull();
- return mCurrentRecord.getInfoValues();
- }
-
- public String[] getFilteringCodes() {
- assertNotNull();
- return mCurrentRecord.getFilteringCodes();
- }
-
- public boolean isFiltered() {
- assertNotNull();
- return mCurrentRecord.isFiltered();
- }
-
-// public boolean hasFilteringCodes() {
-// assertNotNull();
-// return mCurrentRecord.hasFilteringCodes();
-// }
-
- public String getFilterString() {
- assertNotNull();
- return mCurrentRecord.getFilterString();
- }
-
- public VCFHeader getHeader() {
- return mReader.getHeader();
- }
-
- public boolean hasNext() {
- return mReader.hasNext();
- }
-
- /**
- * @return the next element in the iteration.
- * @throws NoSuchElementException - iterator has no more elements.
- */
- public RodVCF next() {
- if (!this.hasNext()) throw new NoSuchElementException("RodVCF next called on iterator with no more elements");
-
- // get the next record
- VCFRecord rec = mReader.next();
-
- // make sure the next VCF record isn't before the current record (we'll accept at the same location, the
- // spec doesn't indicate, and it seems like a valid use case)
- GenomeLoc curPosition = null;
- if (mCurrentRecord != null) curPosition = mCurrentRecord.getLocation();
- if (curPosition != null && rec != null && curPosition.compareTo(rec.getLocation()) > 0)
- throw new StingException("The next VCF record appears to be before the current (current location => " + curPosition.toString() +
- ", the next record position => " + rec.getLocation().toString() + " with line : " + rec.toStringEncoding(mReader.getHeader()) + "). " +
- "Check to make sure the input VCF file is correctly sorted.");
-
- // save off the previous record. This is needed given how iterators are used in the ROD system;
- // we need to save off the last record
- mCurrentRecord = rec;
- return new RodVCF(name, rec, mReader);
- }
-
- public void remove() {
- throw new UnsupportedOperationException("The remove operation is not supported for a VCF rod");
- }
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 4556c7907..11adf5a0b 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -4,6 +4,7 @@ import edu.mit.broad.picard.genotype.DiploidGenotype;
import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broad.tribble.gelitext.GeliTextFeature;
+import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
import org.broadinstitute.sting.gatk.contexts.variantcontext.MutableGenotype;
@@ -16,7 +17,6 @@ import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
import org.broadinstitute.sting.utils.genotype.geli.GeliTextWriter;
import org.broadinstitute.sting.utils.genotype.glf.GLFSingleCall;
import org.broadinstitute.sting.utils.genotype.glf.GLFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.*;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.*;
@@ -46,7 +46,6 @@ public class VariantContextAdaptors {
static {
adaptors.put(DbSNPFeature.class, new DBSnpAdaptor());
- adaptors.put(RodVCF.class, new RodVCFAdaptor());
adaptors.put(VCFRecord.class, new VCFRecordAdaptor());
adaptors.put(PlinkRod.class, new PlinkRodAdaptor());
adaptors.put(HapMapROD.class, new HapMapAdaptor());
@@ -132,23 +131,6 @@ public class VariantContextAdaptors {
}
}
- // --------------------------------------------------------------------------------------------------------------
- //
- // VCF to VariantContext and back again
- //
- // --------------------------------------------------------------------------------------------------------------
-
- private static class RodVCFAdaptor extends VCAdaptor {
- // WARNING: do not use this method if you have anything other than point mutations in your VCF
- VariantContext convert(String name, Object input) {
- return vcfToVariantContext(name, ((RodVCF)input).getRecord(), null);
- }
-
- VariantContext convert(String name, Object input, ReferenceContext ref) {
- return vcfToVariantContext(name, ((RodVCF)input).getRecord(), ref);
- }
- }
-
private static class VCFRecordAdaptor extends VCAdaptor {
// WARNING: do not use this method if you have anything other than point mutations in your VCF
VariantContext convert(String name, Object input) {
@@ -229,7 +211,7 @@ public class VariantContextAdaptors {
double qual = vcf.isMissingQual() ? VariantContext.NO_NEG_LOG_10PERROR : vcf.getNegLog10PError();
- GenomeLoc loc = vcf.getLocation();
+ GenomeLoc loc = GenomeLocParser.createGenomeLoc(vcf.getChr(),vcf.getStart());
if ( vcf.isDeletion() )
loc = GenomeLocParser.createGenomeLoc(loc.getContig(), loc.getStart(), loc.getStart()+refAllele.length()-1);
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java
index 206caea03..431d49ce7 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java
@@ -66,7 +66,6 @@ public class RODTrackBuilder implements RMDTrackBuilder {
Types.put("HapMap", HapMapROD.class);
Types.put("Intervals", IntervalRod.class);
Types.put("GLF", RodGLF.class);
- Types.put("VCF", RodVCF.class);
Types.put("PicardDbSNP", rodPicardDbSNP.class);
Types.put("HapmapVCF", HapmapVCFROD.class);
Types.put("Beagle", BeagleROD.class);
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
index 8e7381ecf..7c9959284 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
@@ -67,8 +67,7 @@ public class TribbleRMDTrackBuilder extends PluginManager implemen
public Map getAvailableTrackNamesAndTypes() {
Map classes = new HashMap();
for (String c : this.pluginsByName.keySet())
- // we're excluding VCF right now
- if (!c.contains("VCF")) classes.put(c,this.pluginsByName.get(c));
+ classes.put(c,this.pluginsByName.get(c));
return classes;
}
@@ -88,15 +87,13 @@ public class TribbleRMDTrackBuilder extends PluginManager implemen
// make a feature reader
FeatureReader reader;
try {
- FeatureCodec codec = this.createByType(targetClass);
-
// check to see if the input file has an index
if (!(new File(inputFile.getAbsolutePath() + linearIndexExtension).canRead())) {
- LinearIndex index = createIndex(inputFile, codec);
- reader = new FeatureReader(inputFile,index, codec);
+ LinearIndex index = createIndex(inputFile, this.createByType(targetClass));
+ reader = new FeatureReader(inputFile,index, this.createByType(targetClass));
}
else {
- reader = new FeatureReader(inputFile,codec);
+ reader = new FeatureReader(inputFile,this.createByType(targetClass));
}
} catch (FileNotFoundException e) {
throw new StingException("Unable to create reader with file " + inputFile, e);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
index cbeb9a297..add373434 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
@@ -26,6 +26,10 @@
package org.broadinstitute.sting.gatk.walkers;
import org.broad.tribble.dbsnp.DbSNPFeature;
+import org.broad.tribble.vcf.VCFGenotypeRecord;
+import org.broad.tribble.vcf.VCFHeader;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@@ -95,8 +99,8 @@ public class VariantsToVCF extends RodWalker {
throw new IllegalStateException("VCF record was created, but no rod data is present");
Object rod = rods.get(0);
- if ( rod instanceof RodVCF )
- samples.addAll(Arrays.asList(((RodVCF)rod).getSampleNames()));
+ if ( rod instanceof VCFRecord )
+ samples.addAll(Arrays.asList(((VCFRecord)rod).getSampleNames()));
else if ( rod instanceof HapMapROD )
samples.addAll(Arrays.asList(((HapMapROD)rod).getSampleIDs()));
else
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Alignability.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Alignability.java
index 8ce4c425d..f4f481c9b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Alignability.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Alignability.java
@@ -1,12 +1,12 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.TabularROD;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.HashMap;
import java.util.Map;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index 85ae80959..48518cfd6 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -25,13 +25,13 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
index 87857ca76..7d35e207c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
@@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.List;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
index 243c49fff..39e072e4d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
@@ -1,12 +1,12 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
index 55939176c..6c9519554 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
@@ -1,10 +1,10 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
index 2a78d26e0..8430f68e5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
@@ -1,12 +1,12 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index 5fcd979cd..3ad9b12ca 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -36,7 +37,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ExtendedPileupElement;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
+
import java.util.*;
import net.sf.samtools.SAMRecord;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
index 90f712bff..edd579490 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
@@ -1,11 +1,11 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.genotype.HardyWeinbergCalculation;
import org.broadinstitute.sting.utils.QualityUtils;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
index 234139a17..3d1a75cc8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
@@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@@ -7,7 +8,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
index d1a14e1c0..1100db5c8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
@@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@@ -7,7 +8,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
index 69c0e3273..07dc64102 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
@@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.List;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
index ebeca20a8..dee2dd145 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
@@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@@ -8,7 +9,6 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index 1645ed20a..1faed4335 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -1,15 +1,14 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
-import java.util.ArrayList;
import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualityAdjustedSecondBaseLod.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualityAdjustedSecondBaseLod.java
index 481945b08..31c738541 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualityAdjustedSecondBaseLod.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualityAdjustedSecondBaseLod.java
@@ -1,11 +1,11 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
index 14e752de9..200d035be 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
@@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@@ -9,8 +11,6 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
import java.util.ArrayList;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
index 5e0017e73..f1b0935b9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
@@ -25,11 +25,11 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
index a251de39b..f4371184e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
@@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@@ -7,7 +8,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index a15dc0001..d447b48ec 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -25,12 +25,14 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
+import org.broad.tribble.vcf.VCFHeader;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
@@ -41,8 +43,6 @@ import org.broadinstitute.sting.utils.classloader.PackageUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
@@ -184,7 +184,7 @@ public class VariantAnnotator extends LocusWalker {
}
}
- if ( variant instanceof RodVCF ) {
+ if ( variant instanceof VCFRecord) {
for(VariantContext annotatedVC : annotatedVCs ) {
vcfWriter.addRecord(VariantContextAdaptors.toVCF(annotatedVC, ref.getBase()));
}
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index 1b7cbc5bb..56f842533 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -26,6 +26,9 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.dbsnp.DbSNPFeature;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
@@ -41,9 +44,6 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.playground.gatk.walkers.annotator.GenomicAnnotation;
import org.broadinstitute.sting.utils.classloader.PackageUtils;
import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
index 7efb0f62c..9eafd8eaf 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
@@ -1,11 +1,11 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+import org.broad.tribble.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFFormatHeaderLine;
import java.util.Map;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
index dff773954..23e079358 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
@@ -1,10 +1,10 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java
index 6546dd26c..bd9210f22 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java
@@ -25,10 +25,13 @@
package org.broadinstitute.sting.gatk.walkers.concordance;
+import org.broad.tribble.vcf.VCFGenotypeRecord;
+import org.broad.tribble.vcf.VCFHeader;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
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.refdata.RodVCF;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.classloader.PackageUtils;
@@ -157,12 +160,14 @@ public class CallsetConcordanceWalker extends RodWalker {
return 0;
// get all of the vcf rods at this locus
- ArrayList vcfRods = new ArrayList();
+ Map vcfRods = new LinkedHashMap();
Iterator rods = rodData.getAllRods().iterator();
while (rods.hasNext()) {
GATKFeature rod = rods.next();
- if ( rod.getUnderlyingObject() instanceof RodVCF )
- vcfRods.add((RodVCF)rod.getUnderlyingObject());
+ if ( rod.getUnderlyingObject() instanceof VCFRecord ) {
+ if (vcfRods.containsKey(rod)) throw new StingException("Duplicate VCF's found");
+ vcfRods.put((VCFRecord)rod.getUnderlyingObject(),rod.getName());
+ }
}
if ( vcfRods.size() == 0 )
@@ -171,12 +176,12 @@ public class CallsetConcordanceWalker extends RodWalker {
// pull out all of the individual calls from the rods and insert into a map based on the
// mapping from rod/sample to uniquified name
HashMap samplesToRecords = new HashMap();
- for ( RodVCF rod : vcfRods ) {
+ for ( VCFRecord rod : vcfRods.keySet() ) {
List records = rod.getVCFGenotypeRecords();
for ( VCFGenotypeRecord vcfRec : records ) {
- String uniquifiedSample = rodNamesToSampleNames.get(new Pair(rod.getName(), vcfRec.getSampleName()));
+ String uniquifiedSample = rodNamesToSampleNames.get(new Pair(vcfRods.get(rod), vcfRec.getSampleName()));
if ( uniquifiedSample == null )
- throw new StingException("Unexpected sample encountered: " + vcfRec.getSampleName() + " in rod " + rod.getName());
+ throw new StingException("Unexpected sample encountered: " + vcfRec.getSampleName() + " in rod " + vcfRods.get(rod));
samplesToRecords.put(uniquifiedSample, vcfRec);
}
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/ConcordanceType.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/ConcordanceType.java
index a1c9ff703..124da2d46 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/ConcordanceType.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/ConcordanceType.java
@@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.walkers.concordance;
+import org.broad.tribble.vcf.VCFGenotypeRecord;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
import java.util.Map;
import java.util.Set;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java
index 5c5623926..7e9826f51 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java
@@ -1,11 +1,11 @@
package org.broadinstitute.sting.gatk.walkers.concordance;
+import org.broad.tribble.vcf.VCFGenotypeRecord;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
import java.util.*;
@@ -103,5 +103,5 @@ public class IndelSubsets implements ConcordanceType {
}
public String getInfoName() { return "IndelSubsets"; }
- public VCFInfoHeaderLine getInfoDescription() { return new VCFInfoHeaderLine(getInfoName(), 1, VCFInfoHeaderLine.INFO_TYPE.String, "Indel-related subsets"); }
+ public VCFInfoHeaderLine getInfoDescription() { return new VCFInfoHeaderLine(getInfoName(), 1, VCFInfoHeaderLine.INFO_TYPE.String, "Indel-related subsets"); }
}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/NWayVenn.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/NWayVenn.java
index 6a6740612..5cb852300 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/NWayVenn.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/NWayVenn.java
@@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.walkers.concordance;
+import org.broad.tribble.vcf.VCFGenotypeRecord;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
import java.util.*;
import java.util.Map.Entry;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java
index 521b618f6..62a53139a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java
@@ -1,9 +1,9 @@
package org.broadinstitute.sting.gatk.walkers.concordance;
+import org.broad.tribble.vcf.VCFGenotypeRecord;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
import java.util.*;
@@ -116,5 +116,5 @@ public class SNPGenotypeConcordance implements ConcordanceType {
}
public String getInfoName() { return "SnpConcordance"; }
- public VCFInfoHeaderLine getInfoDescription() { return new VCFInfoHeaderLine(getInfoName(), 1, VCFInfoHeaderLine.INFO_TYPE.String, "SNP concordance test"); }
+ public VCFInfoHeaderLine getInfoDescription() { return new VCFInfoHeaderLine(getInfoName(), 1, VCFInfoHeaderLine.INFO_TYPE.String, "SNP concordance test"); }
}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java
index e028becae..1e7c9f6eb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java
@@ -1,9 +1,9 @@
package org.broadinstitute.sting.gatk.walkers.concordance;
+import org.broad.tribble.vcf.VCFGenotypeRecord;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
import org.broadinstitute.sting.utils.StingException;
import java.util.*;
@@ -64,5 +64,5 @@ public class SimpleVenn implements ConcordanceType {
}
public String getInfoName() { return "Venn"; }
- public VCFInfoHeaderLine getInfoDescription() { return new VCFInfoHeaderLine(getInfoName(), 1, VCFInfoHeaderLine.INFO_TYPE.String, "2-way Venn split"); }
+ public VCFInfoHeaderLine getInfoDescription() { return new VCFInfoHeaderLine(getInfoName(), 1, VCFInfoHeaderLine.INFO_TYPE.String, "2-way Venn split"); }
}
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
index cf6a3e182..9617d6295 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
@@ -25,7 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.filters;
-import org.apache.commons.jexl.Expression;
+import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
@@ -40,6 +40,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.genotype.vcf.*;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
index 55813a2fa..37fecd640 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
@@ -25,11 +25,11 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
+import org.broad.tribble.vcf.VCFGenotypeRecord;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.genotype.CalledGenotype;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
index 8c1771d8a..b1ec3a81a 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
@@ -1,9 +1,9 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broad.tribble.dbsnp.DbSNPFeature;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.pileup.*;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 88ab0d390..8643a68f0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -25,6 +25,10 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
+import org.broad.tribble.vcf.VCFGenotypeRecord;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
index 54b17e4ea..6959758fc 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
@@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.sequenom;
+import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
@@ -38,6 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.genotype.vcf.*;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java b/java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java
index 030b3375a..d68c00265 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java
@@ -1,13 +1,13 @@
package org.broadinstitute.sting.oneoffprojects.refdata;
+import org.broad.tribble.vcf.VCFHeader;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.refdata.BasicReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFHeader;
import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
import java.io.File;
import java.io.FileNotFoundException;
@@ -23,14 +23,15 @@ public class HapmapVCFROD extends BasicReferenceOrderedDatum implements Iterator
// This is a (hopefully temporary) wrapper class for certain VCF files that we want to protect from
// utilities that grab genotypes or sample names across all VCF files
- private RodVCF rod;
+ private VCFRecord record;
+ private VCFReader reader;
public VCFReader getReader() {
- return rod.getReader();
+ return reader;
}
public VCFRecord getRecord() {
- return rod.getRecord();
+ return record;
}
public HapmapVCFROD(String name) {
@@ -39,85 +40,77 @@ public class HapmapVCFROD extends BasicReferenceOrderedDatum implements Iterator
public HapmapVCFROD(String name, VCFRecord currentRecord, VCFReader reader) {
super(name);
- rod = new RodVCF(name,currentRecord,reader);
- }
-
- public HapmapVCFROD(String name, RodVCF rod) {
- super(name);
- this.rod = rod;
+ this.record = currentRecord;
+ this.reader = reader;
}
public Object initialize(final File source) throws FileNotFoundException {
- rod = new RodVCF(name);
- rod.initialize(source);
- return rod.getHeader();
+ reader = new VCFReader(source);
+ if (reader.hasNext()) record = reader.next();
+ return reader.getHeader();
}
public boolean parseLine(Object obj, String[] args) {
- try {
- return rod.parseLine(obj,args);
- } catch (Exception e) {
- throw new UnsupportedOperationException("Parse line not supported",e);
- }
+ return false;
}
public double getNegLog10PError() {
- return rod.getNegLog10PError();
+ return record.getNegLog10PError();
}
public String getReference() {
- return rod.getReference();
+ return record.getReference();
}
public String toString() {
- return rod.toString();
+ return record.toString();
}
public List getAlternateAlleleList() {
- return rod.getAlternateAlleleList();
+ return record.getAlternateAlleleList();
}
public boolean isDeletion() {
- return rod.isDeletion();
+ return record.isDeletion();
}
public GenomeLoc getLocation() {
- return rod.getLocation();
+ return GenomeLocParser.createGenomeLoc(record.getChr(),record.getStart());
}
public boolean isBiallelic() {
- return rod.isBiallelic();
+ return record.isBiallelic();
}
public boolean isIndel() {
- return rod.isIndel();
+ return record.isIndel();
}
public boolean isSNP() {
- return rod.isSNP();
+ return record.isSNP();
}
public boolean isReference() {
- return rod.isReference();
+ return record.isReference();
}
public double getNonRefAlleleFrequency() {
- return rod.getNonRefAlleleFrequency();
+ return record.getNonRefAlleleFrequency();
}
public char getAlternativeBaseForSNP() {
- return rod.getAlternativeBaseForSNP();
+ return record.getAlternativeBaseForSNP();
}
public boolean isInsertion() {
- return rod.isInsertion();
+ return record.isInsertion();
}
public List getAlleleList() {
- return rod.getAlleleList();
+ return record.getAlleleList();
}
public char getReferenceForSNP() {
- return rod.getReferenceForSNP();
+ return record.getReferenceForSNP();
}
public boolean hasGenotype(DiploidGenotype g) {
@@ -126,29 +119,29 @@ public class HapmapVCFROD extends BasicReferenceOrderedDatum implements Iterator
}
public VCFHeader getHeader() {
- return rod.getHeader();
+ return record.getHeader();
}
public boolean hasNext() {
- return rod.hasNext();
+ return reader.hasNext();
}
public HapmapVCFROD next() {
- return new HapmapVCFROD(name,rod.next());
+ return new HapmapVCFROD(name, record, reader);
}
public void remove() {
- rod.remove();
+ throw new UnsupportedOperationException("Unable to remove");
}
public static HapmapVCFROD createIterator(String name, File file) {
- RodVCF vcf = new RodVCF(name);
+ HapmapVCFROD vcf = new HapmapVCFROD(name);
try {
vcf.initialize(file);
} catch (FileNotFoundException e) {
- throw new StingException("Unable to find file " + file);
+ throw new StingException("Unable to load file",e);
}
- return new HapmapVCFROD(name,vcf);
+ return vcf;
}
}
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java
index 932219db6..0448da9f8 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java
@@ -1,16 +1,16 @@
package org.broadinstitute.sting.oneoffprojects.walkers;
+import org.broad.tribble.vcf.VCFCodec;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import java.util.*;
@@ -22,7 +22,7 @@ import java.util.*;
* Time: 3:25:11 PM
* To change this template use File | Settings | File Templates.
*/
-@Requires(value= DataSource.REFERENCE,referenceMetaData = {@RMD(name="variants",type= RodVCF.class)})
+@Requires(value= DataSource.REFERENCE,referenceMetaData = {@RMD(name="variants",type= VCFCodec.class)})
public class AlleleBalanceHistogramWalker extends LocusWalker, Map>> {
@@ -47,12 +47,11 @@ public class AlleleBalanceHistogramWalker extends LocusWalker
}
public Map map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
- RodVCF vcfRod = tracker.lookup("variants",RodVCF.class);
+ VCFRecord record = tracker.lookup("variants", VCFRecord.class);
- if ( vcfRod == null ) {
+ if ( record == null ) {
return null;
}
- VCFRecord record = vcfRod.getRecord();
return getAlleleBalanceBySample(record,ref,context);
}
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java
index 3ffa8fd11..7d0817c19 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java
@@ -1,15 +1,16 @@
package org.broadinstitute.sting.oneoffprojects.walkers;
+import org.broad.tribble.vcf.VCFHeader;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeatureIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.vcf.*;
@@ -93,12 +94,12 @@ public class IndelAnnotator extends RodWalker{
Object variant = rods.get(0);
- if ( variant instanceof RodVCF ) {
+ if ( variant instanceof VCFRecord) {
RODRecordList annotationList = (refseqIterator == null ? null : refseqIterator.seekForward(ref.getLocus()));
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
annotationString = annotationString.split("\\s+")[0];
- ((RodVCF) variant).getRecord().addInfoField("type",annotationString);
- vcfWriter.addRecord(((RodVCF) variant).getRecord());
+ ((VCFRecord) variant).addInfoField("type",annotationString);
+ vcfWriter.addRecord((VCFRecord) variant);
} else {
throw new StingException("This one-off walker only deals with VCF files.");
}
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
index e6301e3b7..5f143d502 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
@@ -1,11 +1,12 @@
package org.broadinstitute.sting.oneoffprojects.walkers;
+import org.broad.tribble.vcf.VCFHeader;
+import org.broad.tribble.vcf.VCFHeaderLine;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
@@ -13,8 +14,6 @@ import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCFReferenceFixerWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCFReferenceFixerWalker.java
index 1451ab1b4..1e2edef15 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCFReferenceFixerWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCFReferenceFixerWalker.java
@@ -1,12 +1,11 @@
package org.broadinstitute.sting.oneoffprojects.walkers;
+import org.broad.tribble.vcf.VCFHeader;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.RodVCF;
-import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.collections.Pair;
@@ -42,14 +41,13 @@ public class VCFReferenceFixerWalker extends RodWalker {
}
List