@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());
}
}
