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Go around the ROD system for now so that we can just call decodeLoc() for efficiency. Noted that we should go through the ROD system once it gets cleaned up. This means that currently gzipped files are not supported with -L.

This commit is contained in:
Eric Banks 2011-10-26 15:42:53 -04:00
parent 3273c20c98
commit b6ce6ed3f8
1 changed files with 23 additions and 8 deletions
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31
public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
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@ -27,14 +27,19 @@ package org.broadinstitute.sting.commandline;
import com.google.java.contract.Requires;
import net.sf.samtools.util.CloseableIterator;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.readers.AsciiLineReader;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.*;
/**
@ -74,15 +79,25 @@ public final class IntervalBinding<T extends Feature> {
if ( featureIntervals != null ) {
intervals = new ArrayList<GenomeLoc>();
RMDTrackBuilder builder = new RMDTrackBuilder(toolkit.getReferenceDataSource().getReference().getSequenceDictionary(),
toolkit.getGenomeLocParser(),
toolkit.getArguments().unsafe);
FeatureManager.FeatureDescriptor descriptor = new FeatureManager().getByName(featureIntervals.getTribbleType());
CloseableIterator<GATKFeature> iterator = builder.createInstanceOfTrack(descriptor.getCodecClass(), new File(featureIntervals.getSource())).getIterator();
while ( iterator.hasNext() ) {
intervals.add(iterator.next().getLocation());
//RMDTrackBuilder builder = new RMDTrackBuilder(toolkit.getReferenceDataSource().getReference().getSequenceDictionary(),
// toolkit.getGenomeLocParser(),
// toolkit.getArguments().unsafe);
// TODO -- after ROD system cleanup, go through the ROD system so that we can handle things like gzipped files
FeatureCodec codec = new FeatureManager().getByName(featureIntervals.getTribbleType()).getCodec();
try {
FileInputStream fis = new FileInputStream(new File(featureIntervals.getSource()));
AsciiLineReader lineReader = new AsciiLineReader(fis);
codec.readHeader(lineReader);
String line = lineReader.readLine();
while ( line != null ) {
intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(codec.decodeLoc(line)));
line = lineReader.readLine();
}
} catch (IOException e) {
throw new UserException("Problem reading the interval file " + featureIntervals.getSource() + "; " + e.getMessage());
}
iterator.close();
} else {
intervals = IntervalUtils.parseIntervalArguments(toolkit.getGenomeLocParser(), stringIntervals);