109 lines
4.7 KiB
Java
109 lines
4.7 KiB
Java
/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.commandline;
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import com.google.java.contract.Requires;
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import net.sf.samtools.util.CloseableIterator;
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import org.broad.tribble.Feature;
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import org.broad.tribble.FeatureCodec;
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import org.broad.tribble.readers.AsciiLineReader;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
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import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.interval.IntervalUtils;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.IOException;
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import java.util.*;
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/**
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* An IntervalBinding representing a walker argument that gets bound to either a ROD track or interval string.
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*
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* The IntervalBinding<T> is a formal GATK argument that bridges between a walker and
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* the engine to construct intervals for traversal at runtime. The IntervalBinding can
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* either be a RodBinding<T>, a string of one or more intervals, or a file with interval strings.
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* The GATK Engine takes care of initializing the binding when appropriate and determining intervals from it.
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*
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* Note that this class is immutable.
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*/
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public final class IntervalBinding<T extends Feature> {
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private RodBinding<T> featureIntervals;
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private String stringIntervals;
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@Requires({"type != null", "rawName != null", "source != null", "tribbleType != null", "tags != null"})
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public IntervalBinding(Class<T> type, final String rawName, final String source, final String tribbleType, final Tags tags) {
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featureIntervals = new RodBinding<T>(type, rawName, source, tribbleType, tags);
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}
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@Requires({"intervalArgument != null"})
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public IntervalBinding(String intervalArgument) {
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stringIntervals = intervalArgument;
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}
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public String getSource() {
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if ( featureIntervals != null )
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return featureIntervals.getSource();
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return stringIntervals;
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}
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public List<GenomeLoc> getIntervals(GenomeAnalysisEngine toolkit) {
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List<GenomeLoc> intervals;
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if ( featureIntervals != null ) {
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intervals = new ArrayList<GenomeLoc>();
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//RMDTrackBuilder builder = new RMDTrackBuilder(toolkit.getReferenceDataSource().getReference().getSequenceDictionary(),
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// toolkit.getGenomeLocParser(),
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// toolkit.getArguments().unsafe);
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// TODO -- after ROD system cleanup, go through the ROD system so that we can handle things like gzipped files
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FeatureCodec codec = new FeatureManager().getByName(featureIntervals.getTribbleType()).getCodec();
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try {
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FileInputStream fis = new FileInputStream(new File(featureIntervals.getSource()));
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AsciiLineReader lineReader = new AsciiLineReader(fis);
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codec.readHeader(lineReader);
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String line = lineReader.readLine();
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while ( line != null ) {
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intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(codec.decodeLoc(line)));
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line = lineReader.readLine();
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}
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} catch (IOException e) {
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throw new UserException("Problem reading the interval file " + featureIntervals.getSource() + "; " + e.getMessage());
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}
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} else {
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intervals = IntervalUtils.parseIntervalArguments(toolkit.getGenomeLocParser(), stringIntervals);
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}
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return intervals;
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}
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}
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