@ Deprecated public static PCollection < Read > getReadsFromBAMFileSharded ( Pipeline p , PipelineOptions pipelineOptions , OfflineAuth auth , List < Contig > contigs , ReaderOptions options , String BAMFile , ShardingPolicy shardingPolicy ) throws IOException { ReadBAMTransform readBAMSTransform = new ReadBAMTransform ( options ) ; readBAMSTransform . setAuth ( auth ) ; final Storage . Objects storage = Transport . newStorageClient ( pipelineOptions . as ( GCSOptions . class ) ) . build ( ) . objects ( ) ; final List < BAMShard > shardsList = Sharder . shardBAMFile ( storage , BAMFile , contigs , shardingPolicy ) ; PCollection < BAMShard > shards = p . apply ( Create . of ( shardsList ) ) ; return readBAMSTransform . expand ( shards ) ; }
Get reads from a single BAM file by serially reading one shard at a time .