94 lines
4.0 KiB
Java
94 lines
4.0 KiB
Java
|
/*
|
||
|
|
* 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.commandline;
|
||
|
|
|
||
|
|
import com.google.java.contract.Requires;
|
||
|
|
import net.sf.samtools.util.CloseableIterator;
|
||
|
|
import org.broad.tribble.Feature;
|
||
|
|
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.interval.IntervalUtils;
|
||
|
|
|
||
|
|
import java.io.File;
|
||
|
|
import java.util.*;
|
||
|
|
|
||
|
|
/**
|
||
|
|
* An IntervalBinding representing a walker argument that gets bound to either a ROD track or interval string.
|
||
|
|
*
|
||
|
|
* The IntervalBinding<T> is a formal GATK argument that bridges between a walker and
|
||
|
|
* the engine to construct intervals for traversal at runtime. The IntervalBinding can
|
||
|
|
* either be a RodBinding<T>, a string of one or more intervals, or a file with interval strings.
|
||
|
|
* The GATK Engine takes care of initializing the binding when appropriate and determining intervals from it.
|
||
|
|
*
|
||
|
|
* Note that this class is immutable.
|
||
|
|
*/
|
||
|
|
public final class IntervalBinding<T extends Feature> {
|
||
|
|
|
||
|
|
private RodBinding<T> featureIntervals;
|
||
|
|
private String stringIntervals;
|
||
|
|
|
||
|
|
@Requires({"type != null", "rawName != null", "source != null", "tribbleType != null", "tags != null"})
|
||
|
|
public IntervalBinding(Class<T> type, final String rawName, final String source, final String tribbleType, final Tags tags) {
|
||
|
|
featureIntervals = new RodBinding<T>(type, rawName, source, tribbleType, tags);
|
||
|
|
}
|
||
|
|
|
||
|
|
@Requires({"intervalArgument != null"})
|
||
|
|
public IntervalBinding(String intervalArgument) {
|
||
|
|
stringIntervals = intervalArgument;
|
||
|
|
}
|
||
|
|
|
||
|
|
public String getSource() {
|
||
|
|
if ( featureIntervals != null )
|
||
|
|
return featureIntervals.getSource();
|
||
|
|
return stringIntervals;
|
||
|
|
}
|
||
|
|
|
||
|
|
public List<GenomeLoc> getIntervals(GenomeAnalysisEngine toolkit) {
|
||
|
|
List<GenomeLoc> intervals;
|
||
|
|
|
||
|
|
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());
|
||
|
|
}
|
||
|
|
iterator.close();
|
||
|
|
|
||
|
|
} else {
|
||
|
|
intervals = IntervalUtils.parseIntervalArguments(toolkit.getGenomeLocParser(), stringIntervals);
|
||
|
|
}
|
||
|
|
|
||
|
|
return intervals;
|
||
|
|
}
|
||
|
|
}
|