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Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers 

-- Deleted ReadMetaDataTracker
-- Added function to ReadShard to give us the span from the left most position of the reads in the shard to the right most, which is needed for the new view
This commit is contained in:
Mark DePristo 2012-08-29 17:39:32 -04:00
parent 972be8b4a4
commit 1200848bbf
26 changed files with 85 additions and 116 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -34,7 +34,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.*;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.PartitionBy;
import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
@ -247,7 +247,7 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
* @return a linked list with all the reads produced by the clipping operations
*/
@Override
public LinkedList<GATKSAMRecord> map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
public LinkedList<GATKSAMRecord> map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
LinkedList<GATKSAMRecord> mappedReads;
totalReads++;
if (!debugRead.isEmpty() && read.getReadName().contains(debugRead))

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -308,7 +308,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
for( final VariantContext vc : tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()) ) {
if( !allelesToGenotype.contains(vc) ) {
allelesToGenotype.add(vc); // save for later for processing during the ActiveRegion's map call. Should be folded into a ReadMetaDataTracker object
allelesToGenotype.add(vc); // save for later for processing during the ActiveRegion's map call. Should be folded into a RefMetaDataTracker object
}
}
if( tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()).size() > 0 ) {

4
public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
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@ -31,7 +31,7 @@ import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -81,7 +81,7 @@ public class AlignmentValidation extends ReadWalker<Integer,Integer> {
* @return Number of reads aligned by this map (aka 1).
*/
@Override
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
//logger.info(String.format("examining read %s", read.getReadName()));
byte[] bases = read.getReadBases();

21
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java
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@ -27,8 +27,9 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.picard.util.PeekableIterator;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.datasources.reads.ReadShard;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -38,11 +39,11 @@ import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
/** a ROD view for reads. This provides the Read traversals a way of getting a ReadMetaDataTracker */
/** a ROD view for reads. This provides the Read traversals a way of getting a RefMetaDataTracker */
public class ReadBasedReferenceOrderedView implements View {
// a list of the RMDDataState (location->iterators)
private final List<RMDDataState> states = new ArrayList<RMDDataState>(1);
private final static ReadMetaDataTracker EMPTY_TRACKER = new ReadMetaDataTracker();
private final static RefMetaDataTracker EMPTY_TRACKER = new RefMetaDataTracker();
/**
* Used to get genome locs for reads
@ -56,7 +57,7 @@ public class ReadBasedReferenceOrderedView implements View {
private final GenomeLoc shardSpan;
public ReadBasedReferenceOrderedView(final ShardDataProvider provider) {
this(provider.getGenomeLocParser(), provider.getShard().getLocation());
this(provider.getGenomeLocParser(), ((ReadShard)provider.getShard()).getReadsSpan());
provider.register(this);
if ( provider.getReferenceOrderedData() != null && ! shardSpan.isUnmapped() ) {
@ -89,32 +90,32 @@ public class ReadBasedReferenceOrderedView implements View {
}
/**
* create a ReadMetaDataTracker given the current read
* create a RefMetaDataTracker given the current read
*
* @param rec the read
*
* @return a ReadMetaDataTracker for the read, from which you can get ROD -> read alignments
* @return a RefMetaDataTracker for the read, from which you can get ROD -> read alignments
*/
@Requires("rec != null")
@Ensures("result != null")
public ReadMetaDataTracker getReferenceOrderedDataForRead(final SAMRecord rec) {
public RefMetaDataTracker getReferenceOrderedDataForRead(final SAMRecord rec) {
if ( rec.getReadUnmappedFlag() )
// empty RODs for unmapped reads
return new ReadMetaDataTracker();
return new RefMetaDataTracker();
else
return getReferenceOrderedDataForInterval(genomeLocParser.createGenomeLoc(rec));
}
@Requires({"interval != null", "shardSpan.containsP(interval)"})
@Ensures("result != null")
public ReadMetaDataTracker getReferenceOrderedDataForInterval(final GenomeLoc interval) {
public RefMetaDataTracker getReferenceOrderedDataForInterval(final GenomeLoc interval) {
if ( states.isEmpty() ) // optimization for no bindings (common for read walkers)
return EMPTY_TRACKER;
else {
final List<RODRecordList> bindings = new ArrayList<RODRecordList>(states.size());
for ( final RMDDataState state : states )
bindings.add(state.stream.getOverlapping(interval));
return new ReadMetaDataTracker(bindings);
return new RefMetaDataTracker(bindings);
}
}

31
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
View File

@ -7,10 +7,7 @@ import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.*;
/**
*
@ -125,4 +122,30 @@ public class ReadShard extends Shard {
}
return sb.toString();
}
/**
* Get the full span from the start of the left most read to the end of the right most one
*
* Note this may be different than the getLocation() of the shard, as this reflects the
* targeted span, not the actual span of reads
*
* @return the genome loc representing the span of these reads on the genome
*/
public GenomeLoc getReadsSpan() {
if ( isUnmapped() || super.getGenomeLocs() == null || reads.isEmpty() )
return super.getLocation();
else {
int start = Integer.MAX_VALUE;
int stop = Integer.MIN_VALUE;
String contig = null;
for ( final SAMRecord read : reads ) {
contig = read.getReferenceName();
if ( read.getAlignmentStart() < start ) start = read.getAlignmentStart();
if ( read.getAlignmentEnd() > stop ) stop = read.getAlignmentEnd();
}
return parser.createGenomeLoc(contig, start, stop);
}
}
}

51
public/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java
View File

@ -1,51 +0,0 @@
/*
* Copyright (c) 2010. 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;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.datasources.providers.RODMetaDataContainer;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.*;
/**
* @author aaron
* <p/>
* Class ReadMetaDataTracker
* <p/>
* a read-based meta data tracker
*/
public class ReadMetaDataTracker extends RefMetaDataTracker {
public ReadMetaDataTracker() {
super();
}
public ReadMetaDataTracker(Collection<RODRecordList> allBindings) {
super(allBindings);
}
}

4
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
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@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.datasources.providers.ReadBasedReferenceOrd
import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView;
import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -91,7 +91,7 @@ public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,Read
dataProvider.getShard().getReadMetrics().incrementNumIterations();
// if the read is mapped, create a metadata tracker
final ReadMetaDataTracker tracker = read.getReferenceIndex() >= 0 ? rodView.getReferenceOrderedDataForRead(read) : null;
final RefMetaDataTracker tracker = read.getReferenceIndex() >= 0 ? rodView.getReferenceOrderedDataForRead(read) : null;
final boolean keepMeP = walker.filter(refContext, (GATKSAMRecord) read);
if (keepMeP) {

5
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java
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@ -29,9 +29,8 @@ import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.providers.*;
import org.broadinstitute.sting.gatk.datasources.reads.ReadShard;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.nanoScheduler.MapFunction;
import org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler;
@ -142,7 +141,7 @@ public class TraverseReadsNano<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,
//dataProvider.getShard().getReadMetrics().incrementNumIterations();
// if the read is mapped, create a metadata tracker
final ReadMetaDataTracker tracker = read.getReferenceIndex() >= 0 ? rodView.getReferenceOrderedDataForRead(read) : null;
final RefMetaDataTracker tracker = read.getReferenceIndex() >= 0 ? rodView.getReferenceOrderedDataForRead(read) : null;
final boolean keepMeP = walker.filter(refContext, (GATKSAMRecord) read);
if (keepMeP) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
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@ -36,7 +36,7 @@ import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipping.ClippingOp;
@ -299,7 +299,7 @@ public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipRea
* @param read the read itself, as a GATKSAMRecord
* @return the ReadClipper object describing what should be done to clip this read
*/
public ReadClipperWithData map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
public ReadClipperWithData map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES )
read = ReadClipper.revertSoftClippedBases(read);

4
public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java
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@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -179,7 +179,7 @@ public class FlagStat extends ReadWalker<FlagStat.FlagStatus, FlagStat.FlagStatu
@Override
public FlagStatus map( final ReferenceContext ref, final GATKSAMRecord read, final ReadMetaDataTracker metaDataTracker ) {
public FlagStatus map( final ReferenceContext ref, final GATKSAMRecord read, final RefMetaDataTracker metaDataTracker ) {
return new FlagStatus().add(read);
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
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@ -32,7 +32,7 @@ import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
@ -220,7 +220,7 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
* @param read the read itself, as a GATKSAMRecord
* @return the read itself
*/
public GATKSAMRecord map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) {
public GATKSAMRecord map( ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker ) {
return simplifyReads ? read.simplify() : read;
}

5
public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
View File

@ -1,8 +1,7 @@
package org.broadinstitute.sting.gatk.walkers;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/**
@ -27,5 +26,5 @@ public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, Re
}
// Map over the org.broadinstitute.sting.gatk.contexts.AlignmentContext
public abstract MapType map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker);
public abstract MapType map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker);
}

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

@ -33,7 +33,7 @@ import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -64,7 +64,7 @@ public class SplitSamFile extends ReadWalker<SAMRecord, Map<String, SAMFileWrite
logger.info("SplitSamFile version: " + VERSION);
}
public SAMRecord map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
public SAMRecord map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
return read;
}

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

@ -29,7 +29,7 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
@ -140,7 +140,7 @@ public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
}
@Override
public Integer map(ReferenceContext referenceContext, GATKSAMRecord read, ReadMetaDataTracker readMetaDataTracker) {
public Integer map(ReferenceContext referenceContext, GATKSAMRecord read, RefMetaDataTracker RefMetaDataTracker) {
final String rgID = read.getReadGroup().getId();
final PerReadGroupInfo info = readGroupInfo.get(rgID);

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

@ -4,7 +4,7 @@ import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
@ -74,7 +74,7 @@ public class ReadLengthDistribution extends ReadWalker<Integer, Integer> {
}
@Override
public Integer map(ReferenceContext referenceContext, GATKSAMRecord samRecord, ReadMetaDataTracker readMetaDataTracker) {
public Integer map(ReferenceContext referenceContext, GATKSAMRecord samRecord, RefMetaDataTracker RefMetaDataTracker) {
GATKReportTable table = report.getTable("ReadLengthDistribution");
int length = Math.abs(samRecord.getReadLength());

9
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -36,8 +36,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.BAQMode;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.*;
@ -473,7 +472,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
readsActuallyCleaned.clear();
}
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
if ( currentInterval == null ) {
emit(read);
return 0;
@ -540,7 +539,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// TODO -- it would be nice if we could use indels from 454/Ion reads as alternate consenses
}
private void cleanAndCallMap(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
private void cleanAndCallMap(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
if ( readsToClean.size() > 0 ) {
GenomeLoc earliestPossibleMove = getToolkit().getGenomeLocParser().createGenomeLoc(readsToClean.getReads().get(0));
if ( manager.canMoveReads(earliestPossibleMove) )
@ -619,7 +618,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
}
private void populateKnownIndels(ReadMetaDataTracker metaDataTracker, ReferenceContext ref) {
private void populateKnownIndels(RefMetaDataTracker metaDataTracker, ReferenceContext ref) {
for ( final VariantContext vc : metaDataTracker.getValues(known) ) {
if ( indelRodsSeen.contains(vc) )
continue;

5
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
View File

@ -27,12 +27,11 @@ package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.Cigar;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
@ -80,7 +79,7 @@ public class LeftAlignIndels extends ReadWalker<Integer, Integer> {
writer.addAlignment(read);
}
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
// we can not deal with screwy records
if ( read.getReadUnmappedFlag() || read.getCigar().numCigarElements() == 0 ) {
emit(read);

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

@ -39,7 +39,7 @@ import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
import org.broadinstitute.sting.gatk.filters.Platform454Filter;
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
@ -477,7 +477,7 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
@Override
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
// if ( read.getReadName().equals("428EFAAXX090610:2:36:1384:639#0") ) System.out.println("GOT READ");

4
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountBases extends ReadWalker<Integer, Long> {
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
return read.getReadLength();
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java
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@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.samples.Gender;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.gatk.walkers.DataSource;
@ -41,7 +41,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountMales extends ReadWalker<Integer, Integer> {
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
Sample sample = getSampleDB().getSample(read);
return sample.getGender() == Gender.MALE ? 1 : 0;
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java
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@ -4,7 +4,7 @@ import net.sf.samtools.CigarOperator;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
@ -47,7 +47,7 @@ public class CountReadEvents extends ReadWalker<Map<CigarOperator, ArrayList<Int
@Output (doc = "GATKReport table output")
PrintStream out;
public Map<CigarOperator, ArrayList<Integer>> map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
public Map<CigarOperator, ArrayList<Integer>> map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
return ReadUtils.getCigarOperatorForAllBases(read);
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
@ -42,7 +42,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountReads extends ReadWalker<Integer, Integer> implements TreeReducible<Integer> {
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
return 1;
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java
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@ -4,7 +4,7 @@ import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
@ -41,7 +41,7 @@ import java.util.List;
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountTerminusEvent extends ReadWalker<Pair<Long, Long>, Pair<Long, Long>> {
public Pair<Long, Long> map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
public Pair<Long, Long> map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
List<CigarElement> cigarElements = read.getCigar().getCigarElements();
CigarElement lastElement = null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
@ -75,7 +75,7 @@ public class ReadClippingStats extends ReadWalker<ReadClippingStats.ReadClipping
int readLength, nClippingEvents, nClippedBases;
}
public ReadClippingInfo map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
public ReadClippingInfo map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
if ( AlignmentUtils.isReadUnmapped(read) && MAPPED_ONLY)
return null;

4
public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedViewUnitTest.java
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@ -30,7 +30,7 @@ import org.broad.tribble.Feature;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.refdata.RODRecordListImpl;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -283,7 +283,7 @@ public class ReadBasedReferenceOrderedViewUnitTest extends BaseTest {
final ReadBasedReferenceOrderedView view = new ReadBasedReferenceOrderedView(genomeLocParser, span, names, iterators);
for ( final GenomeLoc interval : intervals ) {
final ReadMetaDataTracker tracker = view.getReferenceOrderedDataForInterval(interval);
final RefMetaDataTracker tracker = view.getReferenceOrderedDataForInterval(interval);
for ( int i = 0; i < RODs.size(); i++ ) {
final ReadMetaDataTrackerRODStreamTest test = RODs.get(i);

4
public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java
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@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
@ -123,7 +123,7 @@ class CountBasesInReadPerformanceWalker extends ReadWalker<Integer,Long> {
private long Gs;
private long Ts;
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
for(byte base: read.getReadBases()) {
switch(base) {
case 'A': As++; break;