/*
* The MIT License
*
* Copyright (c) 2009 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 picard.sam.markduplicates.util;
import htsjdk.samtools.util.SortingCollection;
import picard.PicardException;
import java.io.*;
/** Coded for ReadEnds that just outputs the primitive fields and reads them back. */
public class ReadEndsForMarkDuplicatesCodec implements SortingCollection.Codec<ReadEndsForMarkDuplicates> {
private DataInputStream in;
private DataOutputStream out;
public SortingCollection.Codec<ReadEndsForMarkDuplicates> clone() {
return new ReadEndsForMarkDuplicatesCodec();
}
public void setOutputStream(final OutputStream os) { this.out = new DataOutputStream(os); }
public void setInputStream(final InputStream is) { this.in = new DataInputStream(is); }
public DataInputStream getInputStream() {
return in;
}
public DataOutputStream getOutputStream() {
return out;
}
public void encode(final ReadEndsForMarkDuplicates read) {
try {
this.out.writeShort(read.score);
this.out.writeShort(read.libraryId);
this.out.writeByte(read.orientation);
this.out.writeInt(read.read1ReferenceIndex);
this.out.writeInt(read.read1Coordinate);
this.out.writeLong(read.read1IndexInFile);
this.out.writeInt(read.read2ReferenceIndex);
if (read.orientation > ReadEnds.R) {
this.out.writeInt(read.read2Coordinate);
this.out.writeLong(read.read2IndexInFile);
}
this.out.writeShort(read.readGroup);
this.out.writeShort(read.tile);
this.out.writeShort(read.x);
this.out.writeShort(read.y);
this.out.writeByte(read.orientationForOpticalDuplicates);
} catch (final IOException ioe) {
throw new PicardException("Exception writing ReadEnds to file.", ioe);
}
}
public ReadEndsForMarkDuplicates decode() {
final ReadEndsForMarkDuplicates read = new ReadEndsForMarkDuplicates();
try {
// If the first read results in an EOF we've exhausted the stream
try {
read.score = this.in.readShort();
} catch (final EOFException eof) {
return null;
}
read.libraryId = this.in.readShort();
read.orientation = this.in.readByte();
read.read1ReferenceIndex = this.in.readInt();
read.read1Coordinate = this.in.readInt();
read.read1IndexInFile = this.in.readLong();
read.read2ReferenceIndex = this.in.readInt();
if (read.orientation > ReadEnds.R) {
read.read2Coordinate = this.in.readInt();
read.read2IndexInFile = this.in.readLong();
}
read.readGroup = this.in.readShort();
read.tile = this.in.readShort();
read.x = this.in.readShort();
read.y = this.in.readShort();
read.orientationForOpticalDuplicates = this.in.readByte();
return read;
} catch (final IOException ioe) {
throw new PicardException("Exception writing ReadEnds to file.", ioe);
}
}
}