Java Code Examples for htsjdk.samtools.util.BinaryCodec#readString()

The following examples show how to use htsjdk.samtools.util.BinaryCodec#readString() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source File: SAMFileHeader_Utils.java    From cramtools with Apache License 2.0 5 votes vote down vote up 
private static SAMSequenceRecord readSequenceRecord(final BinaryCodec stream, final String source) {
	final int nameLength = stream.readInt();
	if (nameLength <= 1) {
		throw new SAMFormatException("Invalid BAM file header: missing sequence name in file " + source);
	}
	final String sequenceName = stream.readString(nameLength - 1);
	// Skip the null terminator
	stream.readByte();
	final int sequenceLength = stream.readInt();
	return new SAMSequenceRecord(SAMSequenceRecord.truncateSequenceName(sequenceName), sequenceLength);
}
Example 2
Source File: SAMFileHeader_Utils.java    From cramtools with Apache License 2.0 4 votes vote down vote up 
static SAMFileHeader readHeader(final BinaryCodec stream, final ValidationStringency validationStringency,
		final String source) throws IOException {

	final byte[] buffer = new byte[4];
	stream.readBytes(buffer);
	if (!Arrays.equals(buffer, "BAM\1".getBytes())) {
		throw new IOException("Invalid BAM file header");
	}

	final int headerTextLength = stream.readInt();
	final String textHeader = stream.readString(headerTextLength);
	final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec();
	headerCodec.setValidationStringency(validationStringency);
	final SAMFileHeader samFileHeader = headerCodec.decode(new StringLineReader(textHeader), source);

	final int sequenceCount = stream.readInt();
	if (samFileHeader.getSequenceDictionary().size() > 0) {
		// It is allowed to have binary sequences but no text sequences, so
		// only validate if both are present
		if (sequenceCount != samFileHeader.getSequenceDictionary().size()) {
			throw new SAMFormatException("Number of sequences in text header ("
					+ samFileHeader.getSequenceDictionary().size() + ") != number of sequences in binary header ("
					+ sequenceCount + ") for file " + source);
		}
		for (int i = 0; i < sequenceCount; i++) {
			final SAMSequenceRecord binarySequenceRecord = readSequenceRecord(stream, source);
			final SAMSequenceRecord sequenceRecord = samFileHeader.getSequence(i);
			if (!sequenceRecord.getSequenceName().equals(binarySequenceRecord.getSequenceName())) {
				throw new SAMFormatException("For sequence " + i
						+ ", text and binary have different names in file " + source);
			}
			if (sequenceRecord.getSequenceLength() != binarySequenceRecord.getSequenceLength()) {
				throw new SAMFormatException("For sequence " + i
						+ ", text and binary have different lengths in file " + source);
			}
		}
	} else {
		// If only binary sequences are present, copy them into
		// samFileHeader
		final List<SAMSequenceRecord> sequences = new ArrayList<SAMSequenceRecord>(sequenceCount);
		for (int i = 0; i < sequenceCount; i++) {
			sequences.add(readSequenceRecord(stream, source));
		}
		samFileHeader.setSequenceDictionary(new SAMSequenceDictionary(sequences));
	}

	return samFileHeader;
}