com.intel.genomicsdb.GenomicsDBRecordReader.java Source code

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Here is the source code for com.intel.genomicsdb.GenomicsDBRecordReader.java

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/*
 * The MIT License (MIT)
 * Copyright (c) 2016 Intel Corporation
 *
 * 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 com.intel.genomicsdb;

import htsjdk.tribble.CloseableTribbleIterator;
import htsjdk.tribble.Feature;
import org.apache.hadoop.classification.InterfaceAudience;
import org.apache.hadoop.classification.InterfaceStability;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.log4j.Logger;

import java.io.IOException;

@InterfaceAudience.Public
@InterfaceStability.Stable
public class GenomicsDBRecordReader<VCONTEXT extends Feature, SOURCE> extends RecordReader<String, VCONTEXT> {

    private final GenomicsDBFeatureReader<VCONTEXT, SOURCE> featureReader;
    private CloseableTribbleIterator<VCONTEXT> iterator;
    private VCONTEXT currentVariant;
    private long currentKey;

    GenomicsDBRecordReader(GenomicsDBFeatureReader<VCONTEXT, SOURCE> featureReader) {
        this.featureReader = featureReader;
        this.currentKey = -1;
    }

    public void initialize(InputSplit inputSplit, TaskAttemptContext taskAttemptContext)
            throws IOException, InterruptedException {
        initialize();
    }

    private void initialize() throws IOException {
        this.iterator = featureReader.iterator();
    }

    public boolean nextKeyValue() throws IOException, InterruptedException {
        if (this.iterator.hasNext()) {
            this.currentVariant = iterator.next();
            this.currentKey++;
            return true;
        } else
            return false;
    }

    @Override
    public String getCurrentKey() throws IOException, InterruptedException {
        return Long.toString(currentKey);
    }

    public VCONTEXT getCurrentValue() throws IOException, InterruptedException {
        return currentVariant;
    }

    public float getProgress() throws IOException, InterruptedException {
        return 0;
    }

    public void close() throws IOException {
        this.iterator.close();
    }

    public Boolean hasNext() {
        return this.iterator.hasNext();
    }
}