/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 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
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
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package org.broad.igv.sam.reader;
import htsjdk.samtools.*;
import htsjdk.samtools.seekablestream.SeekableStream;
import htsjdk.samtools.util.CloseableIterator;
import org.apache.log4j.Logger;
import org.broad.igv.sam.EmptyAlignmentIterator;
import org.broad.igv.sam.PicardAlignment;
import org.broad.igv.sam.cram.IGVReferenceSource;
import org.broad.igv.util.HttpUtils;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.stream.IGVSeekableBufferedStream;
import org.broad.igv.util.stream.IGVSeekableStreamFactory;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
/**
* A wrapper for SamTextReader that supports query by interval.
*
* @author jrobinso
*/
public class SAMReader implements AlignmentReader<PicardAlignment> {
static Logger log = Logger.getLogger(SAMReader.class);
String samFile;
FeatureIndex featureIndex;
SAMFileHeader header;
List<String> sequenceNames;
private SamReaderFactory factory;
public SAMReader(String samFile) throws IOException {
this(samFile, true);
}
public SAMReader(String samFile, boolean requireIndex) throws IOException {
this.samFile = samFile;
if (requireIndex) {
featureIndex = SamUtils.getIndexFor(samFile);
if (featureIndex == null) {
throw new IndexNotFoundException(samFile);
}
}
factory = SamReaderFactory.makeDefault().
validationStringency(ValidationStringency.SILENT);
loadHeader();
}
public SAMFileHeader getFileHeader() {
return header;
}
public Set<String> getPlatforms() {
return AlignmentReaderFactory.getPlatforms(getFileHeader());
}
private void loadHeader() {
header = getSamReader(samFile, 0).getFileHeader();
}
public CloseableIterator<PicardAlignment> query(final String sequence, final int start, final int end, final boolean contained) {
if (featureIndex == null) {
featureIndex = SamUtils.getIndexFor(samFile);
}
if (featureIndex == null) {
throw new java.lang.UnsupportedOperationException("SAM files must be indexed to support query methods");
}
if (!featureIndex.containsChromosome(sequence)) {
return EmptyAlignmentIterator.getInstance();
}
// If contained == false (include overlaps) we need to adjust the start to
// ensure we get features that extend into this segment.
int startAdjustment = contained ? 0 : featureIndex.getLongestFeature(sequence);
int startTileNumber = Math.max(0, (start - startAdjustment)) / featureIndex.getTileWidth();
FeatureIndex.TileDef seekPos = featureIndex.getTileDef(sequence, startTileNumber);
if (seekPos != null) {
// Skip to the start of the query interval and open a sam file reader
SamReader reader = getSamReader(samFile, seekPos.getStartPosition());
CloseableIterator<SAMRecord> iter = reader.iterator();
return new SAMQueryIterator(sequence, start, end, contained, iter);
}
return EmptyAlignmentIterator.getInstance();
}
private SamReader getSamReader(String samFile, long startPosition) {
SeekableStream stream = null;
try {
stream = IGVSeekableStreamFactory.getInstance().getStreamFor(samFile);
if (startPosition >= 0) {
stream.seek(startPosition);
}
SamInputResource resource = SamInputResource.of(stream);
return factory.open(resource);
} catch (IOException ex) {
log.error("Error opening sam file", ex);
throw new RuntimeException("Error opening: " + samFile, ex);
}
}
public boolean hasIndex() {
if (featureIndex == null) {
getIndex();
}
return featureIndex != null;
}
public void close() throws IOException {
// Nothing to close
}
private FeatureIndex getIndex() {
if (featureIndex == null) {
featureIndex = SamUtils.getIndexFor(samFile);
}
return featureIndex;
}
public List<String> getSequenceNames() {
if (sequenceNames == null) {
FeatureIndex idx = getIndex();
if (idx == null) {
return null;
} else {
sequenceNames = new ArrayList<String>(idx.getIndexedChromosomes());
}
}
return sequenceNames;
}
public CloseableIterator<PicardAlignment> iterator() {
SamReader reader = getSamReader(samFile, -1);
CloseableIterator<SAMRecord> iter = reader.iterator();
return new SAMQueryIterator(iter);
}
}