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this got left off my last commit 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3635 348d0f76-0448-11de-a6fe-93d51630548a
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aaron 2010-06-25 02:42:44 +00:00
parent 1cb8f51f8c
commit f9c7803d4e
1 changed files with 14 additions and 10 deletions
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24
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -26,16 +26,16 @@
package org.broadinstitute.sting.gatk.walkers.coverage; package org.broadinstitute.sting.gatk.walkers.coverage;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import org.broad.tribble.FeatureReader;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.rodRefSeq; import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeatureIterator; import org.broadinstitute.sting.gatk.refdata.tracks.builders.TribbleRMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.*;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.By; import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
@ -414,8 +414,8 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
if (annotationList == null) { return "UNKNOWN"; } if (annotationList == null) { return "UNKNOWN"; }
for(GATKFeature rec : annotationList) { for(GATKFeature rec : annotationList) {
if ( ((rodRefSeq)rec.getUnderlyingObject()).overlapsExonP(target) ) { if ( ((RefSeqFeature)rec.getUnderlyingObject()).overlapsExonP(target) ) {
return ((rodRefSeq)rec.getUnderlyingObject()).getGeneName(); return ((RefSeqFeature)rec.getUnderlyingObject()).getGeneName();
} }
} }
@ -424,9 +424,13 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
} }
private LocationAwareSeekableRODIterator initializeRefSeq() { private LocationAwareSeekableRODIterator initializeRefSeq() {
ReferenceOrderedData<rodRefSeq> refseq = new ReferenceOrderedData<rodRefSeq>("refseq", TribbleRMDTrackBuilder builder = new TribbleRMDTrackBuilder();
refSeqGeneList, rodRefSeq.class); FeatureReader refseq = builder.createFeatureReader(RefSeqCodec.class,refSeqGeneList).first;
return new SeekableRODIterator(new GATKFeatureIterator(refseq.iterator())); try {
return new SeekableRODIterator(new FeatureToGATKFeatureIterator(refseq.iterator(),"refseq"));
} catch (IOException e) {
throw new StingException("Unable to open file " + refSeqGeneList, e);
}
} }
private void printTargetSummary(PrintStream output, Pair<?,DepthOfCoverageStats> intervalStats) { private void printTargetSummary(PrintStream output, Pair<?,DepthOfCoverageStats> intervalStats) {