VcfSliceReducer.java

/*
 * Copyright 2015-2016 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.opencga.storage.hadoop.variant.archive.mr;

import org.apache.hadoop.hbase.client.Put;
import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
import org.apache.hadoop.hbase.mapreduce.TableReducer;
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.protobuf.VcfSliceProtos.VcfSlice;
import org.opencb.biodata.tools.variant.converters.proto.VariantToVcfSliceConverter;
import org.opencb.biodata.tools.variant.converters.proto.VcfSliceToVariantListConverter;
import org.opencb.opencga.storage.hadoop.variant.archive.ArchiveHelper;

import java.io.IOException;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;

/**
 * Created on 15/02/16.
 *
 * @author Jacobo Coll <jacobo167@gmail.com>
 */
public class VcfSliceReducer extends TableReducer<ImmutableBytesWritable, VcfSliceWritable, ImmutableBytesWritable> {

    private ArchiveHelper helper;

    private VcfSliceToVariantListConverter converterFromSlice;
    private VariantToVcfSliceConverter converterToSlice;


    @Override
    protected void setup(Context context) throws IOException, InterruptedException {
        super.setup(context);

        helper = new ArchiveHelper(context.getConfiguration());
        converterFromSlice = new VcfSliceToVariantListConverter(helper.getMeta());
        converterToSlice = new VariantToVcfSliceConverter();
    }

    @Override
    protected void reduce(ImmutableBytesWritable key, Iterable<VcfSliceWritable> values, Context context)
            throws IOException, InterruptedException {

        List<VcfSlice> slices = new LinkedList<>();

        for (VcfSliceWritable vcfSlice : values) {
            slices.add(vcfSlice.get());
        }

        VcfSlice joinedSlice;
        if (slices.size() == 1) {
            joinedSlice = slices.get(0);
        } else {
            List<Variant> variants = new ArrayList<>();
            int slicePosition = 0;
            for (VcfSlice vcfSlice : slices) {
                variants.addAll(converterFromSlice.convert(vcfSlice));
                slicePosition = vcfSlice.getPosition(); //All the positions should be the same
            }
            joinedSlice = converterToSlice.convert(variants, slicePosition);
        }

        context.getCounter("OPENCGA.HBASE", "VCF_REDUCE_COUNT").increment(1);
        context.getCounter("OPENCGA.HBASE", "VCF_REDUCE_COUNT_" + slices.size()).increment(1);

        Put put = helper.wrap(joinedSlice);

        context.write(key, put);


    }

    @Override
    protected void cleanup(Context context) throws IOException, InterruptedException {
        super.cleanup(context);
    }
}