@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());
}
}
