zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Removing obsolete rod; no longer needed given previous addition to SampleUtils. 

JIRA GSA-318


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3572 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-16 20:03:14 +00:00
parent c671864228
commit b75ded61b8
3 changed files with 5 additions and 154 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java
View File

@ -28,7 +28,6 @@ import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
import org.broadinstitute.sting.gatk.refdata.tracks.RODRMDTrack;
import org.broadinstitute.sting.oneoffprojects.refdata.HapmapVCFROD;
import java.io.File;
import java.util.HashMap;
@ -61,7 +60,6 @@ public class RODTrackBuilder implements RMDTrackBuilder {
Types.put("Intervals", IntervalRod.class);
Types.put("GLF", RodGLF.class);
Types.put("PicardDbSNP", rodPicardDbSNP.class);
Types.put("HapmapVCF", HapmapVCFROD.class);
Types.put("Beagle", BeagleROD.class);
Types.put("Plink", PlinkRod.class);
}

147
java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java
View File

@ -1,147 +0,0 @@
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.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.VCFReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Iterator;
import java.util.List;
/*
* Created by IntelliJ IDEA.
* User: chartl
* Date: Jan 29, 2010
*/
public class HapmapVCFROD extends BasicReferenceOrderedDatum implements Iterator<HapmapVCFROD> {
// 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 VCFRecord record;
private VCFReader reader;
public VCFReader getReader() {
return reader;
}
public VCFRecord getRecord() {
return record;
}
public HapmapVCFROD(String name) {
super(name);
}
public HapmapVCFROD(String name, VCFRecord currentRecord, VCFReader reader) {
super(name);
this.record = currentRecord;
this.reader = reader;
}
public Object initialize(final File source) throws FileNotFoundException {
reader = new VCFReader(source);
if (reader.hasNext()) record = reader.next();
return reader.getHeader();
}
public boolean parseLine(Object obj, String[] args) {
return false;
}
public double getNegLog10PError() {
return record.getNegLog10PError();
}
public String getReference() {
return record.getReference();
}
public String toString() {
return record.toString();
}
public List<String> getAlternateAlleleList() {
return record.getAlternateAlleleList();
}
public boolean isDeletion() {
return record.isDeletion();
}
public GenomeLoc getLocation() {
return GenomeLocParser.createGenomeLoc(record.getChr(),record.getStart());
}
public boolean isBiallelic() {
return record.isBiallelic();
}
public boolean isIndel() {
return record.isIndel();
}
public boolean isSNP() {
return record.isSNP();
}
public boolean isReference() {
return record.isReference();
}
public double getNonRefAlleleFrequency() {
return record.getNonRefAlleleFrequency();
}
public char getAlternativeBaseForSNP() {
return record.getAlternativeBaseForSNP();
}
public boolean isInsertion() {
return record.isInsertion();
}
public List<String> getAlleleList() {
return record.getAlleleList();
}
public char getReferenceForSNP() {
return record.getReferenceForSNP();
}
public boolean hasGenotype(DiploidGenotype g) {
return false;
//return rod.hasGenotype(g);
}
public VCFHeader getHeader() {
return record.getHeader();
}
public boolean hasNext() {
return reader.hasNext();
}
public HapmapVCFROD next() {
return new HapmapVCFROD(name, record, reader);
}
public void remove() {
throw new UnsupportedOperationException("Unable to remove");
}
public static HapmapVCFROD createIterator(String name, File file) {
HapmapVCFROD vcf = new HapmapVCFROD(name);
try {
vcf.initialize(file);
} catch (FileNotFoundException e) {
throw new StingException("Unable to load file",e);
}
return vcf;
}
}

10
java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ThousandGenomesAnnotator.java
View File

@ -1,12 +1,12 @@
package org.broadinstitute.sting.oneoffprojects.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.InfoFieldAnnotation;
import org.broadinstitute.sting.oneoffprojects.refdata.HapmapVCFROD;
import java.util.HashMap;
import java.util.Map;
@ -34,17 +34,17 @@ public class ThousandGenomesAnnotator implements InfoFieldAnnotation {
if ( tracker == null )
return null;
HapmapVCFROD pilot1 = tracker.lookup("pilot1",HapmapVCFROD.class);
HapmapVCFROD pilot2 = tracker.lookup("pilot2",HapmapVCFROD.class);
VCFRecord pilot1 = tracker.lookup("pilot1", VCFRecord.class);
VCFRecord pilot2 = tracker.lookup("pilot2", VCFRecord.class);
String result;
if ( pilot1 == null && pilot2 == null) {
result = "0";
} else {
if ( pilot1 != null && ! pilot1.getRecord().isFiltered() ) {
if ( pilot1 != null && ! pilot1.isFiltered() ) {
result = "1";
} else if ( pilot2 != null && !pilot2.getRecord().isFiltered() ) {
} else if ( pilot2 != null && !pilot2.isFiltered() ) {
result = "1";
} else {
result = "0";