org.opencb.hpg.bigdata.tools.alignment.RegionDepthWritable Maven / Gradle / Ivy
/*
* Copyright 2015 OpenCB
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.opencb.hpg.bigdata.tools.alignment;
import java.io.DataInput;
import java.io.DataOutput;
import java.io.IOException;
import org.apache.hadoop.io.Writable;
import org.opencb.biodata.tools.alignment.tasks.RegionDepth;
public class RegionDepthWritable implements Writable {
public RegionDepth regionDepth;
public RegionDepthWritable() { }
public RegionDepthWritable(RegionDepth regionDepth) { setRegionDepth(regionDepth); }
public RegionDepth getRegionDepth() {
return regionDepth;
}
public void setRegionDepth(RegionDepth regionDepth) {
this.regionDepth = regionDepth;
}
@Override
public void write(DataOutput out) throws IOException {
out.writeUTF(regionDepth.chrom);
out.writeLong(regionDepth.position);
out.writeLong(regionDepth.chunk);
out.writeInt(regionDepth.size);
for (int i = 0; i < regionDepth.size; i++) {
out.writeShort(regionDepth.array[i]);
}
}
@Override
public void readFields(DataInput in) throws IOException {
regionDepth = new RegionDepth();
regionDepth.chrom = in.readUTF();
regionDepth.position = in.readLong();
regionDepth.chunk = in.readLong();
regionDepth.size = in.readInt();
regionDepth.array = (regionDepth.size > 0 ? new short[regionDepth.size] : null);
for (int i = 0; i < regionDepth.size; i++) {
regionDepth.array[i] = in.readShort();
}
}
}