org.bgi.flexlab.gaea.framework.tools.mapreduce.BioJob.java Source code

Introduction

Here is the source code for org.bgi.flexlab.gaea.framework.tools.mapreduce.BioJob.java

Source

/*******************************************************************************
 * Copyright (c) 2017, BGI-Shenzhen
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>
 *******************************************************************************/
package org.bgi.flexlab.gaea.framework.tools.mapreduce;

import htsjdk.samtools.SAMFileHeader;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.mapreduce.Mapper;
import org.bgi.flexlab.gaea.data.mapreduce.input.bam.GaeaAnySAMInputFormat;
import org.bgi.flexlab.gaea.data.mapreduce.input.header.SamHdfsFileHeader;
import org.bgi.flexlab.gaea.data.mapreduce.partitioner.WindowsBasedComparator;
import org.bgi.flexlab.gaea.data.mapreduce.partitioner.WindowsBasedPartitioner;
import org.bgi.flexlab.gaea.data.mapreduce.partitioner.WindowsBasedSort;
import org.bgi.flexlab.gaea.data.structure.bam.filter.util.SamRecordFilter;
import org.seqdoop.hadoop_bam.SAMFormat;

import java.io.IOException;

public class BioJob extends Job {

    @SuppressWarnings("deprecation")
    private BioJob(Configuration conf) throws IOException {
        super(conf);
    }

    public static BioJob getInstance() throws IOException {
        return getInstance(new Configuration());
    }

    public static BioJob getInstance(Configuration conf) throws IOException {
        return new BioJob(conf);
    }

    @SuppressWarnings("rawtypes")
    public void setWindowsBasicMapperClass(Class<? extends Mapper> cls, int windowsSize)
            throws IllegalStateException {
        conf.setInt(WindowsBasedMapper.WINDOWS_SIZE, windowsSize);
        setMapperClass(cls);
        setPartitionerClass(WindowsBasedPartitioner.class);
        setGroupingComparatorClass(WindowsBasedComparator.class);
        setSortComparatorClass(WindowsBasedSort.class);
        // setSortComparatorClass(WindowsBasedBasicSort.class);
    }

    @SuppressWarnings("rawtypes")
    public void setWindowsBasicMapperClass(Class<? extends Mapper> cls, int windowsSize, int windowsExtendSize)
            throws IllegalStateException {
        conf.setInt(WindowsBasedMapper.WINDOWS_EXTEND_SIZE, windowsExtendSize);
        setWindowsBasicMapperClass(cls, windowsSize);
    }

    public void setOnlyBaseRecalibrator(boolean bqsr) {
        conf.setBoolean(WindowsBasedMapper.BASERECALIBRATOR_ONLY, bqsr);
    }

    public void setWindowsBasicMapperClass(@SuppressWarnings("rawtypes") Class<? extends Mapper> cls,
            int windowsSize, int windowsExtendSize, boolean multiSample) throws IllegalStateException {
        if (multiSample)
            setMultipleSample();
        setWindowsBasicMapperClass(cls, windowsSize, windowsExtendSize);
    }

    public void setMultipleSample() {
        conf.setBoolean(WindowsBasedMapper.MULTIPLE_SAMPLE, true);
    }

    /*
     * set windows based mapper filter
     */
    public void setFilterClass(Class<? extends SamRecordFilter> cls) {
        conf.setClass(WindowsBasedMapper.SAM_RECORD_FILTER, cls, SamRecordFilter.class);
    }

    public void setOutputKeyValue(Class<?> mapKeyClass, Class<?> mapValueClass, Class<?> reduceKeyClass,
            Class<?> reduceValueClass) {
        setMapOutputKeyClass(mapKeyClass);
        setMapOutputValueClass(mapValueClass);
        setOutputKeyClass(reduceKeyClass);
        setOutputValueClass(reduceValueClass);
    }

    public void setOutputKeyValue(Class<?> keyClass, Class<?> valueClass) {
        setOutputKeyClass(keyClass);
        setOutputValueClass(valueClass);
    }

    /*
     * set sam or bam inputformat
     */
    public void setAnySamInputFormat(SAMFormat fmt) {
        conf.set(GaeaAnySAMInputFormat.SAM_FORMAT_FOR_ALL_PATH, fmt.toString());
        setInputFormatClass(GaeaAnySAMInputFormat.class);
    }

    public SAMFileHeader setHeader(Path input, Path output) {
        try {
            return SamHdfsFileHeader.loadHeader(input, conf, output);
        } catch (IOException e) {
            throw new RuntimeException(e.toString());
        }
    }

    public void setHeader(String headerPath) {
        conf.set(SamHdfsFileHeader.BAM_HEADER_FILE_NAME, headerPath);
    }
}