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;
}