/*
* Copyright (c) 2012 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.gatk.utils.sam;
import htsjdk.samtools.*;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
/**
* User: hanna
* Date: Jun 11, 2009
* Time: 9:35:31 AM
* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
* Software and documentation are copyright 2005 by the Broad Institute.
* All rights are reserved.
*
* Users acknowledge that this software is supplied without any warranty or support.
* The Broad Institute is not responsible for its use, misuse, or
* functionality.
*/
/**
* Pass specified reads into the given walker.
*/
public class ArtificialSAMFileReader extends SAMFileReader {
/**
* The parser, for GenomeLocs.
*/
private final GenomeLocParser genomeLocParser;
/**
* Backing data store of reads.
*/
private final List<SAMRecord> reads;
private SAMFileHeader customHeader = null;
/**
* Construct an artificial SAM file reader.
* @param sequenceDictionary sequence dictionary used to initialize our GenomeLocParser
* @param reads Reads to use as backing data source.
*/
public ArtificialSAMFileReader(SAMSequenceDictionary sequenceDictionary,SAMRecord... reads) {
super( createEmptyInputStream(),true );
this.genomeLocParser = new GenomeLocParser(sequenceDictionary);
this.reads = Arrays.asList(reads);
}
/**
* Construct an artificial SAM file reader with the given SAM file header
*
* @param customHeader Header that should be returned by calls to getFileHeader() on this reader
* @param reads Reads to use as backing data source.
*/
public ArtificialSAMFileReader( SAMFileHeader customHeader, SAMRecord... reads ) {
super(createEmptyInputStream(),true);
this.customHeader = customHeader;
this.genomeLocParser = new GenomeLocParser(customHeader.getSequenceDictionary());
this.reads = Arrays.asList(reads);
}
@Override
public SAMFileHeader getFileHeader() {
if ( customHeader != null ) {
return customHeader;
}
return super.getFileHeader();
}
/**
* @{inheritDoc}
*/
@Override
public SAMRecordIterator query(final String sequence, final int start, final int end, final boolean contained) {
GenomeLoc region = genomeLocParser.createGenomeLoc(sequence, start, end);
List<SAMRecord> coveredSubset = new ArrayList<SAMRecord>();
for( SAMRecord read: reads ) {
GenomeLoc readPosition = genomeLocParser.createGenomeLoc(read);
if( contained && region.containsP(readPosition) ) coveredSubset.add(read);
else if( !contained && readPosition.overlapsP(region) ) coveredSubset.add(read);
}
final Iterator<SAMRecord> iterator = coveredSubset.iterator();
return new SAMRecordIterator() {
public boolean hasNext() { return iterator.hasNext(); }
public SAMRecord next() { return iterator.next(); }
public void close() {}
public void remove() { iterator.remove(); }
public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder) { return this; }
};
}
@Override
public SAMRecordIterator iterator() {
return new SAMRecordIterator() {
private final Iterator<SAMRecord> iterator = reads.iterator();
public boolean hasNext() { return iterator.hasNext(); }
public SAMRecord next() { return iterator.next(); }
public void close() {}
public void remove() { iterator.remove(); }
public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder) { return this; }
};
}
/**
* Builds an empty input stream for faking out the sam file reader.
* Derive it from a string so that, in the future, it might be possible
* to fake the text of a sam file from samtools output, et.c
* @return Stream that returns no characters.
*/
private static InputStream createEmptyInputStream() {
try {
byte[] byteArray = "".getBytes("ISO-8859-1");
return new ByteArrayInputStream(byteArray);
}
catch( UnsupportedEncodingException ex ) {
throw new ReviewedGATKException("Unable to build empty input stream",ex);
}
}
}