@Override
public void initialize(InputSplit spl, TaskAttemptContext ctx) throws IOException {
// This method should only be called once (see Hadoop API). However,
// there seems to be disagreement between implementations that call
// initialize() and Hadoop-BAM's own code that relies on
// {@link BAMInputFormat} to call initialize() when the reader is
// created. Therefore we add this check for the time being.
if (isInitialized) close();
isInitialized = true;
final Configuration conf = ctx.getConfiguration();
final FileVirtualSplit split = (FileVirtualSplit) spl;
final Path file = split.getPath();
final FileSystem fs = file.getFileSystem(conf);
this.stringency = SAMHeaderReader.getValidationStringency(conf);
final FSDataInputStream in = fs.open(file);
final SAMFileHeader header = SAMHeaderReader.readSAMHeaderFrom(in, conf);
codec = new BAMRecordCodec(header);
in.seek(0);
bci =
new BlockCompressedInputStream(
new WrapSeekable<FSDataInputStream>(in, fs.getFileStatus(file).getLen(), file));
virtualStart = split.getStartVirtualOffset();
fileStart = virtualStart >>> 16;
virtualEnd = split.getEndVirtualOffset();
bci.seek(virtualStart);
codec.setInputStream(bci);
if (BAMInputFormat.DEBUG_BAM_SPLITTER) {
final long recordStart = virtualStart & 0xffff;
System.err.println(
"XXX inizialized BAMRecordReader byte offset: "
+ fileStart
+ " record offset: "
+ recordStart);
}
keepReadPairsTogether =
SortOrder.queryname.equals(header.getSortOrder())
&& conf.getBoolean(BAMInputFormat.KEEP_PAIRED_READS_TOGETHER_PROPERTY, false);
readPair = false;
lastOfPair = false;
intervals = BAMInputFormat.getIntervals(conf);
if (intervals != null) {
overlapDetector = new OverlapDetector<>(0, 0);
overlapDetector.addAll(intervals, intervals);
}
}
public BAMSplitGuesser(SeekableStream ss, InputStream headerStream, Configuration conf)
throws IOException {
inFile = ss;
buf = ByteBuffer.allocate(8);
buf.order(ByteOrder.LITTLE_ENDIAN);
referenceSequenceCount =
SAMHeaderReader.readSAMHeaderFrom(headerStream, conf).getSequenceDictionary().size();
bamCodec = new BAMRecordCodec(null, new LazyBAMRecordFactory());
}