@Override
protected void reduce(ChromosomeRegion key, Iterable<SAMRecordWritable> values, Context context)
throws IOException, InterruptedException {
super.reduce(key, values, context);
try {
Logger.DEBUG("Processing key: " + key);
// wrappers to call external programs
PreprocessingTools tools = new PreprocessingTools(bin);
GATKTools gatk = new GATKTools(ref, bin);
gatk.setContext(context);
tools.setContext(context);
gatk.setThreads(threads);
if (java != null) {
gatk.setJava(java);
tools.setJava(java);
}
processAlignments(values, context, tools, gatk);
} catch (URISyntaxException | QualityException | ProcessException ex) {
Logger.EXCEPTION(ex);
throw new InterruptedException(ex.getMessage());
}
}
@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;
}
}
