org.bgi.flexlab.gaea.tools.bamqualtiycontrol.report.BamReport.java Source code

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Here is the source code for org.bgi.flexlab.gaea.tools.bamqualtiycontrol.report.BamReport.java

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/*******************************************************************************
 * 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.tools.bamqualtiycontrol.report;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.util.LineReader;
import org.bgi.flexlab.gaea.data.structure.reference.ReferenceShare;
import org.bgi.flexlab.gaea.tools.mapreduce.bamqualitycontrol.BamQualityControlOptions;

import java.io.IOException;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;

public class BamReport {

    public static void getOutput(BamQualityControlOptions options, Configuration conf, Path oPath)
            throws IOException {
        ReportBuilder reportBuilder = new ReportBuilder();
        ResultReport reportType;
        ReferenceShare genome = new ReferenceShare();
        genome.loadChromosomeList(options.getReferenceSequencePath());

        if ((options.getRegion() != null) || (options.getBedfile() != null))
            reportType = new RegionResultReport(options, conf);
        else
            reportType = new WholeGenomeResultReport(options);

        Map<String, ResultReport> reports = new ConcurrentHashMap<String, ResultReport>();
        FileSystem fs = oPath.getFileSystem(conf);
        FileStatus filelist[] = fs.listStatus(oPath);
        for (int i = 0; i < filelist.length; i++) {
            if (!filelist[i].isDir() && !filelist[i].getPath().toString().startsWith("_")) {
                FSDataInputStream reader = fs.open(filelist[i].getPath());
                LineReader lineReader = new LineReader(reader, conf);
                Text line = new Text();
                while (lineReader.readLine(line) > 0) {
                    String lineString = line.toString();
                    if (line.getLength() == 0) {
                        continue;
                    }

                    if (lineString.contains("sample:")) {
                        String sample = line.toString().split(":")[1];
                        if (!reports.containsKey(sample)) {
                            reports.put(sample, reportType);
                            reportBuilder.setReportChoice(reportType);
                            reportBuilder.initReports(sample);
                        } else {
                            reportType = reports.get(sample);
                            reportBuilder.setReportChoice(reportType);
                        }
                    }
                    reportBuilder.parseReport(lineReader, line, genome);

                }
                lineReader.close();
                reader.close();
            }
        }

        for (String sampleName : reports.keySet()) {
            System.err.println("sample:" + sampleName);
            ResultReport report = reports.get(sampleName);
            report.write(fs, sampleName);
        }

        fs.close();
    }
}