@Override
public void flushStream() {
try {
// close the input stream
reads1.getSTDINWriter().flush();
if (isPaired) reads2.getSTDINWriter().flush();
} catch (IOException ex) {
Logger.EXCEPTION(ex);
}
}
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
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()));
}
}
@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;
}
@Override
public InputStream getSTDOUTStream() {
return samxe.getSTDOUTStream();
}
/** @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();
}