@Override
public PCollection<KV<K, CoGbkResult>> apply(KeyedPCollectionTuple<K> input) {
if (input.isEmpty()) {
throw new IllegalArgumentException("must have at least one input to a KeyedPCollections");
}
// First build the union coder.
// TODO: Look at better integration of union types with the
// schema specified in the input.
List<Coder<?>> codersList = new ArrayList<>();
for (TaggedKeyedPCollection<K, ?> entry : input.getKeyedCollections()) {
codersList.add(getValueCoder(entry.pCollection));
}
UnionCoder unionCoder = UnionCoder.of(codersList);
Coder<K> keyCoder = input.getKeyCoder();
KvCoder<K, RawUnionValue> kVCoder = KvCoder.of(keyCoder, unionCoder);
PCollectionList<KV<K, RawUnionValue>> unionTables = PCollectionList.empty(input.getPipeline());
// TODO: Use the schema to order the indices rather than depending
// on the fact that the schema ordering is identical to the ordering from
// input.getJoinCollections().
int index = -1;
for (TaggedKeyedPCollection<K, ?> entry : input.getKeyedCollections()) {
index++;
PCollection<KV<K, RawUnionValue>> unionTable =
makeUnionTable(index, entry.pCollection, kVCoder);
unionTables = unionTables.and(unionTable);
}
PCollection<KV<K, RawUnionValue>> flattenedTable =
unionTables.apply(Flatten.<KV<K, RawUnionValue>>pCollections());
PCollection<KV<K, Iterable<RawUnionValue>>> groupedTable =
flattenedTable.apply(GroupByKey.<K, RawUnionValue>create());
CoGbkResultSchema tupleTags = input.getCoGbkResultSchema();
PCollection<KV<K, CoGbkResult>> result =
groupedTable.apply(
ParDo.of(new ConstructCoGbkResultFn<K>(tupleTags)).named("ConstructCoGbkResultFn"));
result.setCoder(KvCoder.of(keyCoder, CoGbkResultCoder.of(tupleTags, unionCoder)));
return result;
}
@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());
}
