@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);
}
}
/**
* Create a common SAMFileWriter for use with GATK tools.
*
* @param outputFile - if this file has a .cram extension then a reference is required. Can not be
* null.
* @param referenceFile - the reference source to use. Can not be null if a output file has a
* .cram extension.
* @param header - header to be used for the output writer
* @param preSorted - if true then the records must already be sorted to match the header sort
* order
* @param createOutputBamIndex - if true an index will be created for .BAM and .CRAM files
* @param createMD5 - if true an MD5 file will be created
* @return SAMFileWriter
*/
public static SAMFileWriter createCommonSAMWriter(
final File outputFile,
final File referenceFile,
final SAMFileHeader header,
final boolean preSorted,
boolean createOutputBamIndex,
final boolean createMD5) {
Utils.nonNull(outputFile);
Utils.nonNull(header);
if (createOutputBamIndex && header.getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
logger.warn(
"Skipping index file creation for: "
+ outputFile.getAbsolutePath()
+ ". Index file creation requires reads in coordinate sorted order.");
createOutputBamIndex = false;
}
final SAMFileWriterFactory factory =
new SAMFileWriterFactory().setCreateIndex(createOutputBamIndex).setCreateMd5File(createMD5);
return ReadUtils.createCommonSAMWriterFromFactory(
factory, outputFile, referenceFile, header, preSorted);
}