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();
}
@Override
protected void setup(Context context) throws IOException, InterruptedException {
super.setup(context);
isFirstAttempt = taskId.endsWith("_0");
isRNA = HalvadeConf.getIsRNA(context.getConfiguration());
scc = HalvadeConf.getSCC(context.getConfiguration(), isRNA);
sec = HalvadeConf.getSEC(context.getConfiguration(), isRNA);
try {
gff = HalvadeFileUtils.downloadGFF(context, taskId);
} catch (URISyntaxException ex) {
Logger.EXCEPTION(ex);
throw new InterruptedException("Error when downloading GFF file");
}
filterBedFile = HalvadeConf.getFilterBed(context.getConfiguration());
filterDBsnp = HalvadeConf.getFilterDBSnp(context.getConfiguration());
useUnifiedGenotyper = HalvadeConf.getUseUnifiedGenotyper(context.getConfiguration());
redistribute = HalvadeConf.getRedistribute(context.getConfiguration());
containers = HalvadeConf.getMapContainerCount(context.getConfiguration());
tasksLeft = Integer.parseInt(context.getConfiguration().get("mapred.map.tasks")) - taskNr;
// get task number:
if (redistribute && tasksLeft < containers) {
threads = 6;
}
}