@Override public void write(K ignored, SAMRecordWritable rec) { writeAlignment(rec.get()); } }
@Override public void write(K ignored, SAMRecordWritable rec) { writeAlignment(rec.get()); } }
@Override public void write(K ignored, SAMRecordWritable rec) { writeAlignment(rec.get()); } }
@Override public void write(K ignored, SAMRecordWritable rec) throws IOException { writeAlignment(rec.get()); } }
@Override public void write(K ignored, SAMRecordWritable rec) throws IOException { writeAlignment(rec.get()); } }
@Override public void write(K ignored, SAMRecordWritable rec) { writeAlignment(rec.get()); } }
@Override public void write(K ignored, SAMRecordWritable rec) { writeAlignment(rec.get()); } }
@Override public void write(K ignored, SAMRecordWritable rec) { writeAlignment(rec.get()); } }
@Override public void write(K ignored, SAMRecordWritable rec) throws IOException { writeAlignment(rec.get()); } }
@Override public void map(LongWritable key, SAMRecordWritable value, Context context) throws IOException, InterruptedException { // ChunkKey newKey; SAMRecord sam = value.get(); if (sam.getReadUnmappedFlag()) { System.out.println("Empty block"); // do nothing // newKey = new ChunkKey(new String("*"), (long) 0); } else { // long start_chunk = sam.getAlignmentStart() / RegionDepth.CHUNK_SIZE; // long end_chunk = sam.getAlignmentEnd() / RegionDepth.CHUNK_SIZE; // newKey = new ChunkKey(sam.getReferenceName(), start_chunk); SAMRecordToAvroReadAlignmentBiConverter converter = samRecord2ReadAlignmentConverter; ReadAlignment readAlignment = converter.to(sam); AvroKey<ReadAlignment> newKey = new AvroKey<>(readAlignment); //context.write(newKey, value); context.write(newKey, NullWritable.get()); } } }
private List<SAMRecord> getSAMRecordsFromSplit(BAMInputFormat inputFormat, InputSplit split) throws Exception { RecordReader<LongWritable, SAMRecordWritable> reader = inputFormat .createRecordReader(split, taskAttemptContext); reader.initialize(split, taskAttemptContext); List<SAMRecord> records = new ArrayList<SAMRecord>(); while (reader.nextKeyValue()) { SAMRecord r = reader.getCurrentValue().get(); records.add(r); } return records; } }