@Override
public void validate(PCollection<KV<K, V>> input) {
try {
GroupByKey.applicableTo(input);
} catch (IllegalStateException e) {
throw new IllegalStateException("Unable to create a side-input view from input", e);
}
}
@Override
public PCollection<KV<ReferenceShard, Iterable<GATKRead>>> apply(PCollection<GATKRead> input) {
PCollection<KV<ReferenceShard, GATKRead>> keyReadByReferenceShard =
input.apply(
ParDo.of(
new DoFn<GATKRead, KV<ReferenceShard, GATKRead>>() {
private static final long serialVersionUID = 1L;
@Override
public void processElement(ProcessContext c) throws Exception {
// Apply our reference window function to each read before deciding which
// reference shard it belongs to.
ReferenceShard shard =
ReferenceShard.getShardNumberFromInterval(
referenceWindowFunction.apply(c.element()));
c.output(KV.of(shard, c.element()));
}
})
.named("KeyReadByRefShard"));
return keyReadByReferenceShard.apply(GroupByKey.<ReferenceShard, GATKRead>create());
}
