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");
}
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();
}