ReadStatsWritable.java

/*
 * 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.sequence.stats;

import org.apache.hadoop.io.Writable;
import org.opencb.biodata.tools.alignment.stats.SequenceInfo;
import org.opencb.biodata.tools.alignment.stats.SequenceStats;

import java.io.DataInput;
import java.io.DataOutput;
import java.io.IOException;
import java.util.HashMap;

public class ReadStatsWritable implements Writable {

    private SequenceStats stats;

    public ReadStatsWritable() { }

    public ReadStatsWritable(SequenceStats stats) {
        setStats(stats);
    }

    @Override
    public void write(DataOutput out) throws IOException {
        out.writeInt(stats.numSeqs);
        out.writeInt(stats.numA);
        out.writeInt(stats.numT);
        out.writeInt(stats.numG);
        out.writeInt(stats.numC);
        out.writeInt(stats.numN);
        out.writeInt(stats.minSeqLength);
        out.writeInt(stats.maxSeqLength);
        out.writeInt(stats.accSeqQual);

        out.writeInt(stats.lengthMap.size());
        for (int key:stats.lengthMap.keySet()) {
            out.writeInt(key);
            out.writeInt(stats.lengthMap.get(key));
        }

        out.writeInt(stats.infoMap.size());
        for (int key:stats.infoMap.keySet()) {
            out.writeInt(key);
            final SequenceInfo info = stats.infoMap.get(key);
            out.writeInt(info.numA);
            out.writeInt(info.numT);
            out.writeInt(info.numG);
            out.writeInt(info.numC);
            out.writeInt(info.numN);
            out.writeInt(info.numQual);
            out.writeInt(info.accQual);
        }

        // I don't knwo why it does not work
        // new FastqKmersWritable(kmers).write(out);
        out.writeInt(stats.kmers.kvalue);

        out.writeInt(stats.kmers.kmersMap.size());
        for (String key:stats.kmers.kmersMap.keySet()) {
            out.writeUTF(key);
            out.writeInt(stats.kmers.kmersMap.get(key));
        }
    }

    @Override
    public void readFields(DataInput in) throws IOException {
        int size, key;
        SequenceInfo info;

        stats = new SequenceStats();
        stats.numSeqs = in.readInt();
        stats.numA = in.readInt();
        stats.numT = in.readInt();
        stats.numG = in.readInt();
        stats.numC = in.readInt();
        stats.numN = in.readInt();
        stats.minSeqLength = in.readInt();
        stats.maxSeqLength = in.readInt();
        stats.accSeqQual = in.readInt();

        size = in.readInt();
        stats.lengthMap = new HashMap<>(size);
        for (int i = 0; i < size; i++) {
            stats.lengthMap.put(in.readInt(), in.readInt());
        }

        size = in.readInt();
        stats.infoMap = new HashMap<>(size);
        for (int i = 0; i < size; i++) {
            key = in.readInt();
            info = new SequenceInfo();
            info.numA = in.readInt();
            info.numT = in.readInt();
            info.numG = in.readInt();
            info.numC = in.readInt();
            info.numN = in.readInt();
            info.numQual = in.readInt();
            info.accQual = in.readInt();
            stats.infoMap.put(key, info);
        }

        // I don't knwo why it does not work
        //new FastqKmersWritable(kmers).readFields(in);
        stats.kmers.kvalue = in.readInt();

        size = in.readInt();
        stats.kmers.kmersMap = new HashMap<>(size);
        for (int i = 0; i < size; i++) {
            stats.kmers.kmersMap.put(in.readUTF(), in.readInt());
        }
    }

    public SequenceStats getStats() {
        return stats;
    }

    public void setStats(SequenceStats stats) {
        this.stats = stats;
    }

}