/*
* Copyright (C) 2014 ddecap
*
* 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 be.ugent.intec.halvade.tools;
import be.ugent.intec.halvade.hadoop.mapreduce.HalvadeCounters;
import be.ugent.intec.halvade.utils.CommandGenerator;
import be.ugent.intec.halvade.utils.HalvadeFileUtils;
import be.ugent.intec.halvade.utils.Logger;
import be.ugent.intec.halvade.utils.HalvadeConf;
import be.ugent.intec.halvade.utils.ProcessBuilderWrapper;
import be.ugent.intec.halvade.utils.SAMStreamHandler;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.net.URISyntaxException;
import org.apache.hadoop.mapreduce.Mapper;
/**
*
* @author ddecap
*/
public class BWAAlnInstance extends AlignerInstance {
private static BWAAlnInstance instance;
private ProcessBuilderWrapper reads1;
private ProcessBuilderWrapper reads2;
private ProcessBuilderWrapper samxe;
private SAMStreamHandler ssh;
private BufferedWriter fastqFile1;
private BufferedWriter fastqFile2;
private String taskId;
private String alnCustomArgs;
private BWAAlnInstance(Mapper.Context context, String bin) throws IOException, URISyntaxException {
super(context, bin);
taskId = context.getTaskAttemptID().toString();
taskId = taskId.substring(taskId.indexOf("m_"));
ref = HalvadeFileUtils.downloadBWAIndex(context, taskId);
alnCustomArgs = HalvadeConf.getCustomArgs(context.getConfiguration(), "bwa", "aln");
}
public int feedLine(String line, int read) throws IOException, InterruptedException {
if(read == 1 || !isPaired) {
fastqFile1.write(line + "\n");
return feedLine(line, reads1);
} else if (read == 2) {
fastqFile2.write(line + "\n");
if(threads > 1) return feedLine(line, reads2);
else return 0;
}
return -1;
}
protected String getFileName(String dir, String id, boolean isSai, int read) {
String outFile = dir;
if(isSai) {
if(read == 1) {
outFile += read1File + id + ".sai";
} else if (read == 2) {
outFile += read2File + id + ".sai";
} else return null;
} else {
if(read == 1) {
outFile += read1File + id + ".fastq";
} else if (read == 2) {
outFile += read2File + id + ".fastq";
} else return null;
}
return outFile;
}
@Override
protected void startAligner(Mapper.Context context) throws IOException, InterruptedException {
if(redistribute) {
getIdleCores(context);
Logger.DEBUG("Redistributing cores: using " + threads);
}
int threadsToUse = threads;
if (isPaired && threadsToUse > 1 ) threadsToUse /= 2;
String[] command1 = CommandGenerator.bwaAln(bin, ref, "/dev/stdin", getFileName(tmpdir, taskId, true, 1), threadsToUse, alnCustomArgs);
reads1 = new ProcessBuilderWrapper(command1, bin);
reads1.setThreads(threadsToUse);
reads1.startProcess(null, System.err);
// check if alive.
if(!reads1.isAlive())
throw new ProcessException("BWA aln", reads1.getExitState());
File file1 = new File(getFileName(tmpdir, taskId, false, 1));
if (!file1.exists()) {
file1.createNewFile();
}
fastqFile1 = new BufferedWriter(new FileWriter(file1.getAbsoluteFile()));
if(isPaired) {
if(threads > 1) {
String[] command2 = CommandGenerator.bwaAln(bin, ref, "/dev/stdin", getFileName(tmpdir, taskId, true, 2), threadsToUse, alnCustomArgs);
reads2 = new ProcessBuilderWrapper(command2, bin);
reads2.setThreads(threadsToUse);
reads2.startProcess(null, System.err);
if(!reads2.isAlive())
throw new ProcessException("BWA aln", reads2.getExitState());
}
File file2 = new File(getFileName(tmpdir, taskId,false, 2));
if (!file2.exists()) {
file2.createNewFile();
}
fastqFile2 = new BufferedWriter(new FileWriter(file2.getAbsoluteFile()));
}
}
/**
*
* @return 1 is running, 0 is completed, -1 is error
*/
@Override
public int getState() {
if (isPaired & threads > 1)
return reads1.getState() & reads2.getState();
else
return reads1.getState();
}
private void closeBWAAln() throws InterruptedException {
try {
// close the input stream
reads1.getSTDINWriter().flush();
reads1.getSTDINWriter().close();
fastqFile1.close();
if(isPaired) {
fastqFile2.close();
if(threads > 1) {
reads2.getSTDINWriter().flush();
reads2.getSTDINWriter().close();
}
}
} catch (IOException ex) {
Logger.EXCEPTION(ex);
throw new ProcessException("BWA aln", -1);
}
int error = reads1.waitForCompletion();
if(error != 0)
throw new ProcessException("BWA aln", error);
context.getCounter(HalvadeCounters.TIME_BWA_ALN).increment(reads1.getExecutionTime());
if(isPaired) {
if(threads == 1) {
String[] command2 = CommandGenerator.bwaAln(bin, ref, getFileName(tmpdir, taskId,false, 2), getFileName(tmpdir, taskId, true, 2),
threads, alnCustomArgs);
reads2 = new ProcessBuilderWrapper(command2, bin);
reads2.setThreads(threads);
reads2.startProcess(null, System.err);
if(!reads2.isAlive())
throw new ProcessException("BWA aln", reads2.getExitState());
}
error = reads2.waitForCompletion();
if(error != 0)
throw new ProcessException("BWA aln", error);
context.getCounter(HalvadeCounters.TIME_BWA_ALN).increment(reads2.getExecutionTime());
}
}
private void startBWASamXe() throws InterruptedException {
String customArgs = HalvadeConf.getCustomArgs(context.getConfiguration(), "bwa", "sampe");
String[] command = CommandGenerator.bwaSamXe(bin, ref,
getFileName(tmpdir, taskId, true, 1),
getFileName(tmpdir, taskId, false, 1),
getFileName(tmpdir, taskId, true, 2),
getFileName(tmpdir, taskId, false, 2),
isPaired, threads, customArgs);
samxe = new ProcessBuilderWrapper(command, bin);
samxe.startProcess(null, System.err);
if(!samxe.isAlive())
throw new ProcessException("BWA samXe", samxe.getExitState());
// make a SAMstream handler
ssh = new SAMStreamHandler(instance, context, false);
ssh.start();
}
@Override
public void closeAligner() throws InterruptedException {
// close last BWA aln
closeBWAAln();
// but now start sampe/samse
startBWASamXe();
ssh.join();
int error = samxe.waitForCompletion();
if(error != 0)
throw new ProcessException("BWA samXe", error);
context.getCounter(HalvadeCounters.TIME_BWA_SAMPE).increment(samxe.getExecutionTime());
//remove all temporary fastq/sai files
HalvadeFileUtils.removeLocalFile(keep, getFileName(tmpdir, taskId, true, 1), context, HalvadeCounters.FOUT_BWA_TMP);
HalvadeFileUtils.removeLocalFile(keep, getFileName(tmpdir, taskId, false, 1), context, HalvadeCounters.FOUT_BWA_TMP);
HalvadeFileUtils.removeLocalFile(keep, getFileName(tmpdir, taskId, true, 2), context, HalvadeCounters.FOUT_BWA_TMP);
HalvadeFileUtils.removeLocalFile(keep, getFileName(tmpdir, taskId, false, 2), context, HalvadeCounters.FOUT_BWA_TMP);
instance = null;
}
static public BWAAlnInstance getBWAInstance(Mapper.Context context, String bin) throws IOException, InterruptedException, URISyntaxException {
if(instance == null) {
instance = new BWAAlnInstance(context, bin);
instance.startAligner(context);
}
BWAAlnInstance.context = context;
Logger.DEBUG("Started BWA");
return instance;
}
@Override
public InputStream getSTDOUTStream() {
return samxe.getSTDOUTStream();
}
@Override
public void flushStream() {
try {
// close the input stream
reads1.getSTDINWriter().flush();
if(isPaired) reads2.getSTDINWriter().flush();
} catch (IOException ex) {
Logger.EXCEPTION(ex);
}
}
}
