@Override
protected void map(
LongWritable ignored,
SAMRecordWritable wrec,
Mapper<LongWritable, SAMRecordWritable, Text, SAMRecordWritable>.Context ctx)
throws InterruptedException, IOException {
Utils.correctSAMRecordForMerging(wrec.get(), ContextUtil.getConfiguration(ctx));
ctx.write(new Text(wrec.get().getReadName()), wrec);
}
@Override
protected void reduce(
Text key,
Iterable<SAMRecordWritable> records,
Reducer<Text, SAMRecordWritable, Text, SAMRecordWritable>.Context ctx)
throws IOException, InterruptedException {
// Non-primary records are simply written out, but as long as we can find
// two primaries, pair them up.
final SAMFileHeader header =
Utils.getSAMHeaderMerger(ContextUtil.getConfiguration(ctx)).getMergedHeader();
final Iterator<SAMRecordWritable> it = records.iterator();
while (it.hasNext()) {
SAMRecordWritable a = it.next();
if (a.get().getNotPrimaryAlignmentFlag()) {
ctx.write(key, a);
continue;
}
// Cache the record since the iterator does its own caching, meaning
// that after another it.next() we would have a == b.
wrec.set(a.get());
a = wrec;
SAMRecordWritable b = null;
while (it.hasNext()) {
b = it.next();
if (!b.get().getNotPrimaryAlignmentFlag()) break;
ctx.write(key, b);
}
if (b == null) {
// No more primaries, so just write the unpaired one as-is.
ctx.write(key, a);
break;
}
a.get().setHeader(header);
b.get().setHeader(header);
SamPairUtil.setMateInfo(a.get(), b.get(), header);
ctx.write(key, a);
ctx.write(key, b);
}
}