case BAM: return bamIF.createRecordReader(split, ctx); case CRAM: return cramIF.createRecordReader(split, ctx); default: assert false; return null;
case BAM: return bamIF.createRecordReader(split, ctx); case CRAM: return cramIF.createRecordReader(split, ctx); default: assert false; return null;
case BAM: return bamIF.createRecordReader(split, ctx); case CRAM: return cramIF.createRecordReader(split, ctx); default: assert false; return null;
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; } }