@Override
public void processElement(ProcessContext c) throws Exception {
String dest = c.element();
logger.info("Saving to " + dest);
Iterable<GATKRead> reads = c.sideInput(iterableView);
OutputStream outputStream = BucketUtils.createFile(dest, c.getPipelineOptions());
try (SAMFileWriter writer =
new SAMFileWriterFactory().makeBAMWriter(header, false, outputStream)) {
for (GATKRead r : reads) {
final SAMRecord sr = r.convertToSAMRecord(header);
writer.addAlignment(sr);
}
}
}
@Override
public <T> T sideInput(PCollectionView<T> view) {
return context.sideInput(view);
}