use of htsjdk.samtools.util.BinaryCodec in project gatk by broadinstitute.
the class SparkUtils method writeBAMHeaderToStream.
/**
* Private helper method for {@link #convertHeaderlessHadoopBamShardToBam} that takes a SAMFileHeader and writes it
* to the provided `OutputStream`, correctly encoded for the BAM format and preceded by the BAM magic bytes.
*
* @param samFileHeader SAM header to write
* @param outputStream stream to write the SAM header to
*/
private static void writeBAMHeaderToStream(final SAMFileHeader samFileHeader, final OutputStream outputStream) {
final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, null);
final BinaryCodec outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
final String headerString;
final Writer stringWriter = new StringWriter();
new SAMTextHeaderCodec().encode(stringWriter, samFileHeader, true);
headerString = stringWriter.toString();
outputBinaryCodec.writeBytes(ReadUtils.BAM_MAGIC);
// calculate and write the length of the SAM file header text and the header text
outputBinaryCodec.writeString(headerString, true, false);
// write the sequences binarily. This is redundant with the text header
outputBinaryCodec.writeInt(samFileHeader.getSequenceDictionary().size());
for (final SAMSequenceRecord sequenceRecord : samFileHeader.getSequenceDictionary().getSequences()) {
outputBinaryCodec.writeString(sequenceRecord.getSequenceName(), true, true);
outputBinaryCodec.writeInt(sequenceRecord.getSequenceLength());
}
try {
blockCompressedOutputStream.flush();
} catch (final IOException ioe) {
throw new RuntimeIOException(ioe);
}
}
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