From 1200848bbfb7069f898e1933ed687a0e18f56e0a Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 29 Aug 2012 17:39:32 -0400 Subject: [PATCH] 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 --- .../compression/reducereads/ReduceReads.java | 4 +- .../haplotypecaller/HaplotypeCaller.java | 2 +- .../sting/alignment/AlignmentValidation.java | 4 +- .../ReadBasedReferenceOrderedView.java | 21 ++++---- .../gatk/datasources/reads/ReadShard.java | 31 +++++++++-- .../gatk/refdata/ReadMetaDataTracker.java | 51 ------------------- .../sting/gatk/traversals/TraverseReads.java | 4 +- .../gatk/traversals/TraverseReadsNano.java | 5 +- .../sting/gatk/walkers/ClipReads.java | 4 +- .../sting/gatk/walkers/FlagStat.java | 4 +- .../sting/gatk/walkers/PrintReads.java | 4 +- .../sting/gatk/walkers/ReadWalker.java | 5 +- .../sting/gatk/walkers/SplitSamFile.java | 4 +- .../diagnostics/ReadGroupProperties.java | 4 +- .../diagnostics/ReadLengthDistribution.java | 4 +- .../gatk/walkers/indels/IndelRealigner.java | 9 ++-- .../gatk/walkers/indels/LeftAlignIndels.java | 5 +- .../walkers/indels/SomaticIndelDetector.java | 4 +- .../sting/gatk/walkers/qc/CountBases.java | 4 +- .../sting/gatk/walkers/qc/CountMales.java | 4 +- .../gatk/walkers/qc/CountReadEvents.java | 4 +- .../sting/gatk/walkers/qc/CountReads.java | 4 +- .../gatk/walkers/qc/CountTerminusEvent.java | 4 +- .../gatk/walkers/qc/ReadClippingStats.java | 4 +- ...ReadBasedReferenceOrderedViewUnitTest.java | 4 +- .../reads/GATKWalkerBenchmark.java | 4 +- 26 files changed, 85 insertions(+), 116 deletions(-) delete mode 100644 public/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java index 177050667..d1ec9c474 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java @@ -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, ReduceRea * @return a linked list with all the reads produced by the clipping operations */ @Override - public LinkedList map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) { + public LinkedList map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) { LinkedList mappedReads; totalReads++; if (!debugRead.isEmpty() && read.getReadName().contains(debugRead)) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index 845fc68a6..3d41b7233 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -308,7 +308,7 @@ public class HaplotypeCaller extends ActiveRegionWalker 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 ) { diff --git a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java index e8eea5ff0..b903b9f7d 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java +++ b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java @@ -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 { * @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(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java index 054758101..adf1b34df 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java @@ -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 states = new ArrayList(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 bindings = new ArrayList(states.size()); for ( final RMDDataState state : states ) bindings.add(state.stream.getOverlapping(interval)); - return new ReadMetaDataTracker(bindings); + return new RefMetaDataTracker(bindings); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java index f5a4cb4cf..9e1c12186 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java @@ -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); + } + } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java deleted file mode 100644 index cfea5901e..000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java +++ /dev/null @@ -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 - *

- * Class ReadMetaDataTracker - *

- * a read-based meta data tracker - */ -public class ReadMetaDataTracker extends RefMetaDataTracker { - public ReadMetaDataTracker() { - super(); - } - - public ReadMetaDataTracker(Collection allBindings) { - super(allBindings); - } -} diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java index 2dc0444b2..3b712c973 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java @@ -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 extends TraversalEngine,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) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java index 4215230b8..081c6b8fc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java @@ -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 extends TraversalEngine, //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) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java index 4eaa16692..e63dbcabd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java @@ -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 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; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java index 77e3af93f..42fbb32bd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java @@ -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 extends Walker { } @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); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java index 1dc8a7ec1..2b84cccc9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java @@ -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 { } @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()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index e6eddc0b7..d9b71f938 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -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 { 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 { // 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 { } } - 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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java index 6b9bd04d2..21b3b71d8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java @@ -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 { 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); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java index 3965a63fb..7c73f59e9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java @@ -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 { @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"); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java index 0c323934e..9954a25e8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java @@ -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 { - public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { + public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { return read.getReadLength(); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java index bc178119d..f2e4cf1ad 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java @@ -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 { - 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; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java index 80845c447..80afd19fa 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java @@ -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(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { + public Map> map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { return ReadUtils.getCigarOperatorForAllBases(read); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java index d33db2925..72bda03e9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java @@ -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 implements TreeReducible { - public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { + public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { return 1; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java index 971b5bb85..09d239126 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java @@ -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> { - public Pair map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { + public Pair map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { List cigarElements = read.getCigar().getCigarElements(); CigarElement lastElement = null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java index 16d614afc..ec4f081a6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java @@ -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 { 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;