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Cleanup of codec locations. No more dbSNPHelper 

-- refdata/features now in utils/codecs with the other codecs
-- Deleted dbsnpHelper.  rsID function now in VCFutils.  Remaining code either deleted or put into VariantContextAdaptors
-- Many associated import updates due to code move
This commit is contained in:
Mark DePristo 2011-08-18 10:02:46 -04:00
parent 9c17d54cb6
commit c2287c93d7
28 changed files with 163 additions and 268 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

72
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -1,10 +1,11 @@
package org.broadinstitute.sting.gatk.refdata;
import net.sf.samtools.util.SequenceUtil;
import org.broad.tribble.Feature;
import org.broad.tribble.annotation.Strand;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broad.tribble.gelitext.GeliTextFeature;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
@ -92,6 +93,67 @@ public class VariantContextAdaptors {
// --------------------------------------------------------------------------------------------------------------
private static class DBSnpAdaptor implements VCAdaptor {
private static boolean isSNP(DbSNPFeature feature) {
return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact");
}
private static boolean isMNP(DbSNPFeature feature) {
return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range");
}
private static boolean isInsertion(DbSNPFeature feature) {
return feature.getVariantType().contains("insertion");
}
private static boolean isDeletion(DbSNPFeature feature) {
return feature.getVariantType().contains("deletion");
}
private static boolean isIndel(DbSNPFeature feature) {
return isInsertion(feature) || isDeletion(feature) || isComplexIndel(feature);
}
public static boolean isComplexIndel(DbSNPFeature feature) {
return feature.getVariantType().contains("in-del");
}
/**
* 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 static List<String> getAlternateAlleleList(DbSNPFeature feature) {
List<String> ret = new ArrayList<String>();
for (String allele : getAlleleList(feature))
if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele);
return ret;
}
/**
* 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 static List<String> getAlleleList(DbSNPFeature feature) {
List<String> alleleList = new ArrayList<String>();
// add ref first
if ( feature.getStrand() == Strand.POSITIVE )
alleleList = Arrays.asList(feature.getObserved());
else
for (String str : feature.getObserved())
alleleList.add(SequenceUtil.reverseComplement(str));
if ( alleleList.size() > 0 && alleleList.contains(feature.getNCBIRefBase())
&& !alleleList.get(0).equals(feature.getNCBIRefBase()) )
Collections.swap(alleleList, alleleList.indexOf(feature.getNCBIRefBase()), 0);
return alleleList;
}
/**
* Converts non-VCF formatted dbSNP records to VariantContext.
* @return DbSNPFeature.
@ -102,18 +164,18 @@ public class VariantContextAdaptors {
@Override
public VariantContext convert(String name, Object input, ReferenceContext ref) {
DbSNPFeature dbsnp = (DbSNPFeature)input;
if ( ! Allele.acceptableAlleleBases(DbSNPHelper.getReference(dbsnp)) )
if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) )
return null;
Allele refAllele = Allele.create(DbSNPHelper.getReference(dbsnp), true);
Allele refAllele = Allele.create(dbsnp.getNCBIRefBase(), true);
if ( DbSNPHelper.isSNP(dbsnp) || DbSNPHelper.isIndel(dbsnp) || DbSNPHelper.isMNP(dbsnp) || dbsnp.getVariantType().contains("mixed") ) {
if ( isSNP(dbsnp) || isIndel(dbsnp) || isMNP(dbsnp) || dbsnp.getVariantType().contains("mixed") ) {
// add the reference allele
List<Allele> alleles = new ArrayList<Allele>();
alleles.add(refAllele);
// add all of the alt alleles
boolean sawNullAllele = refAllele.isNull();
for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) {
for ( String alt : getAlternateAlleleList(dbsnp) ) {
if ( ! Allele.acceptableAlleleBases(alt) ) {
//System.out.printf("Excluding dbsnp record %s%n", dbsnp);
return null;

169
public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java
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@ -1,169 +0,0 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.features;
import net.sf.samtools.util.SequenceUtil;
import org.broad.tribble.annotation.Strand;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
/**
* this class contains static helper methods for DbSNP
*/
public class DbSNPHelper {
private DbSNPHelper() {} // don't make a DbSNPHelper
public static String rsIDOfFirstRealVariant(List<VariantContext> VCs, VariantContext.Type type) {
if ( VCs == null )
return null;
String rsID = null;
for ( VariantContext vc : VCs ) {
if ( vc.getType() == type ) {
rsID = vc.getID();
break;
}
}
return rsID;
}
/**
* get the -1 * (log 10 of the error value)
*
* @return the log based error estimate
*/
public static double getNegLog10PError(DbSNPFeature feature) {
return 4; // -log10(0.0001)
}
//
// What kind of variant are we?
//
// ----------------------------------------------------------------------
public static boolean isSNP(DbSNPFeature feature) {
return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact");
}
public static boolean isMNP(DbSNPFeature feature) {
return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range");
}
public static String toMediumString(DbSNPFeature feature) {
String s = String.format("%s:%d:%s:%s", feature.getChr(), feature.getStart(), feature.getRsID(), Utils.join("",feature.getObserved()));
if (isSNP(feature)) s += ":SNP";
if (isIndel(feature)) s += ":Indel";
if (isHapmap(feature)) s += ":Hapmap";
if (is2Hit2Allele(feature)) s += ":2Hit";
return s;
}
public static boolean isInsertion(DbSNPFeature feature) {
return feature.getVariantType().contains("insertion");
}
public static boolean isDeletion(DbSNPFeature feature) {
return feature.getVariantType().contains("deletion");
}
public static boolean isIndel(DbSNPFeature feature) {
return DbSNPHelper.isInsertion(feature) || DbSNPHelper.isDeletion(feature) || DbSNPHelper.isComplexIndel(feature);
}
public static boolean isComplexIndel(DbSNPFeature feature) {
return feature.getVariantType().contains("in-del");
}
public static boolean isHapmap(DbSNPFeature feature) {
return feature.getValidationStatus().contains("by-hapmap");
}
public static boolean is2Hit2Allele(DbSNPFeature feature) {
return feature.getValidationStatus().contains("by-2hit-2allele");
}
public static boolean is1000genomes(DbSNPFeature feature) {
return feature.getValidationStatus().contains("by-1000genomes");
}
public static boolean isMQ1(DbSNPFeature feature) {
return feature.getWeight() == 1;
}
/**
* 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 static List<String> getAlternateAlleleList(DbSNPFeature feature) {
List<String> ret = new ArrayList<String>();
for (String allele : getAlleleList(feature))
if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele);
return ret;
}
public static boolean onFwdStrand(DbSNPFeature feature) {
return feature.getStrand() == Strand.POSITIVE;
}
public static String getReference(DbSNPFeature feature) {
return feature.getNCBIRefBase();
}
public static String toSimpleString(DbSNPFeature feature) {
return String.format("%s:%s:%s", feature.getRsID(), feature.getObserved(), (feature.getStrand() == Strand.POSITIVE) ? "+" : "-");
}
/**
* 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 static List<String> getAlleleList(DbSNPFeature feature) {
List<String> alleleList = new ArrayList<String>();
// add ref first
if ( onFwdStrand(feature) )
alleleList = Arrays.asList(feature.getObserved());
else
for (String str : feature.getObserved())
alleleList.add(SequenceUtil.reverseComplement(str));
if ( alleleList.size() > 0 && alleleList.contains(getReference(feature)) && !alleleList.get(0).equals(getReference(feature)) )
Collections.swap(alleleList, alleleList.indexOf(getReference(feature)), 0);
return alleleList;
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
View File

@ -26,7 +26,6 @@
package org.broadinstitute.sting.gatk.walkers;
import org.broad.tribble.Feature;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
@ -34,9 +33,6 @@ import org.broadinstitute.sting.commandline.RodBinding;
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.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -29,15 +29,11 @@ import org.broadinstitute.sting.commandline.RodBinding;
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.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationInterfaceManager;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -158,7 +154,7 @@ public class VariantAnnotatorEngine {
private void annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map<String, Object> infoAnnotations) {
for ( Map.Entry<RodBinding<VariantContext>, String> dbSet : dbAnnotations.entrySet() ) {
if ( dbSet.getValue().equals(VCFConstants.DBSNP_KEY) ) {
String rsID = DbSNPHelper.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType());
String rsID = VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType());
infoAnnotations.put(VCFConstants.DBSNP_KEY, rsID != null);
// annotate dbsnp id if available and not already there
if ( rsID != null && (!vc.hasID() || vc.getID().equals(VCFConstants.EMPTY_ID_FIELD)) )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
View File

@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -32,8 +32,8 @@ 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.SeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
View File

@ -39,9 +39,9 @@ import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.features.refseq.Transcript;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
import org.broadinstitute.sting.utils.codecs.refseq.Transcript;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
View File

@ -32,7 +32,7 @@ import org.broadinstitute.sting.commandline.RodBinding;
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.features.sampileup.SAMPileupFeature;
import org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
View File

@ -14,9 +14,8 @@ import org.broadinstitute.sting.commandline.RodBinding;
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.features.table.TableFeature;
import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.BaseUtils;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -33,7 +33,6 @@ 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.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.*;
@ -120,7 +119,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )
return 0;
String rsID = dbsnp == null ? null : DbSNPHelper.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP);
String rsID = dbsnp == null ? null : VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP);
Collection<VariantContext> contexts = getVariantContexts(tracker, ref);

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata.features.beagle;
package org.broadinstitute.sting.utils.codecs.beagle;
/*
* Copyright (c) 2010 The Broad Institute
*

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java → public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java
View File

@ -22,7 +22,7 @@
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.features.beagle;
package org.broadinstitute.sting.utils.codecs.beagle;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.utils.variantcontext.Allele;

3
public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
View File

@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.refdata.features.refseq;
package org.broadinstitute.sting.utils.codecs.refseq;
import org.apache.commons.io.filefilter.FalseFileFilter;
import org.broad.tribble.Feature;
import org.broad.tribble.TribbleException;
import org.broad.tribble.readers.LineReader;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java → public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata.features.refseq;
package org.broadinstitute.sting.utils.codecs.refseq;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;

106
public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/Transcript.java → public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java
View File

@ -1,53 +1,53 @@
package org.broadinstitute.sting.gatk.refdata.features.refseq;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.HasGenomeLocation;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: asivache
* Date: Sep 22, 2009
* Time: 5:22:30 PM
* To change this template use File | Settings | File Templates.
*/
public interface Transcript extends HasGenomeLocation {
/** Returns id of the transcript (RefSeq NM_* id) */
public String getTranscriptId();
/** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
public int getStrand();
/** Returns transcript's full genomic interval (includes all exons with UTRs) */
public GenomeLoc getLocation();
/** Returns genomic interval of the coding sequence (does not include
* UTRs, but still includes introns, since it's a single interval on the DNA)
*/
public GenomeLoc getCodingLocation();
/** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc,
* but the implementation can decide otherwise)
*/
public String getGeneName();
/** Number of exons in this transcript */
public int getNumExons();
/** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */
public GenomeLoc getExonLocation(int n);
/** Returns the list of all exons in this transcript, as genomic intervals */
public List<GenomeLoc> getExons();
/** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */
public boolean overlapsP (GenomeLoc that);
/** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript.
* NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
* but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript.
* @see #overlapsExonP
*/
public boolean overlapsCodingP (GenomeLoc that);
/** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */
public boolean overlapsExonP (GenomeLoc that);
}
package org.broadinstitute.sting.utils.codecs.refseq;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.HasGenomeLocation;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: asivache
* Date: Sep 22, 2009
* Time: 5:22:30 PM
* To change this template use File | Settings | File Templates.
*/
public interface Transcript extends HasGenomeLocation {
/** Returns id of the transcript (RefSeq NM_* id) */
public String getTranscriptId();
/** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
public int getStrand();
/** Returns transcript's full genomic interval (includes all exons with UTRs) */
public GenomeLoc getLocation();
/** Returns genomic interval of the coding sequence (does not include
* UTRs, but still includes introns, since it's a single interval on the DNA)
*/
public GenomeLoc getCodingLocation();
/** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc,
* but the implementation can decide otherwise)
*/
public String getGeneName();
/** Number of exons in this transcript */
public int getNumExons();
/** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */
public GenomeLoc getExonLocation(int n);
/** Returns the list of all exons in this transcript, as genomic intervals */
public List<GenomeLoc> getExons();
/** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */
public boolean overlapsP (GenomeLoc that);
/** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript.
* NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
* but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript.
* @see #overlapsExonP
*/
public boolean overlapsCodingP (GenomeLoc that);
/** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */
public boolean overlapsExonP (GenomeLoc that);
}

4
public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.features.sampileup;
package org.broadinstitute.sting.utils.codecs.sampileup;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
@ -35,7 +35,7 @@ import java.util.ArrayList;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import static org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature.VariantType;
import static org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature.VariantType;
/**
* A Tribble encoder / decoder for SAM pileup data.

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java → public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.features.sampileup;
package org.broadinstitute.sting.utils.codecs.sampileup;
import net.sf.samtools.util.StringUtil;
import org.broad.tribble.Feature;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java
View File

@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.features.samread;
package org.broadinstitute.sting.utils.codecs.samread;
import net.sf.samtools.Cigar;
import net.sf.samtools.TextCigarCodec;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadFeature.java → public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java
View File

@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.features.samread;
package org.broadinstitute.sting.utils.codecs.samread;
import org.broad.tribble.Feature;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata.features.table;
package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata.features.table;
package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature;
import org.broad.tribble.readers.LineReader;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java → public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata.features.table;
package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.utils.GenomeLoc;

15
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
View File

@ -180,4 +180,19 @@ public class VCFUtils {
return new HashSet<VCFHeaderLine>(map.values());
}
public static String rsIDOfFirstRealVariant(List<VariantContext> VCs, VariantContext.Type type) {
if ( VCs == null )
return null;
String rsID = null;
for ( VariantContext vc : VCs ) {
if ( vc.getType() == type ) {
rsID = vc.getID();
break;
}
}
return rsID;
}
}

2
public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
View File

@ -26,7 +26,6 @@
package org.broadinstitute.sting.commandline;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.testng.Assert;
@ -35,7 +34,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import javax.script.Bindings;
import java.util.List;
import java.util.EnumSet;
/**

2
public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
View File

@ -10,7 +10,7 @@ import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;

2
public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;

2
public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java
View File

@ -31,7 +31,7 @@ import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GenomeLoc;

4
public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
View File

@ -29,8 +29,8 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.refdata.features.table.BedTableCodec;
import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
import org.broadinstitute.sting.utils.codecs.table.BedTableCodec;
import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;