Java Code Examples for htsjdk.samtools.SAMFileHeader#getSequence()

The following examples show how to use htsjdk.samtools.SAMFileHeader#getSequence() . 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: CreateIntervalsFiles.java    From Drop-seq with MIT License 5 votes vote down vote up 
/**
 * Create a SAM header with a subset of the sequences
 * @param samHeader header to be subsetted
 * @param sequenceNames sequences to include
 * @return clone of the original header, but with only the named sequences
 */
private static SAMFileHeader createSubsetSamHeader(final SAMFileHeader samHeader, final List<String> sequenceNames) {
    final SAMFileHeader ret = samHeader.clone();
    final List<SAMSequenceRecord> sequenceRecords = new ArrayList<>(sequenceNames.size());
    for (final String sequence: sequenceNames) {
        final SAMSequenceRecord sequenceRecord = ret.getSequence(sequence);
        if (sequenceRecord == null)
throw new RuntimeException("Sequence '" + sequence + "' specified on command line but not found in sequence dictionary");
        sequenceRecords.add(sequenceRecord);
    }
    ret.getSequenceDictionary().setSequences(sequenceRecords);
    return ret;
}
Example 2
Source File: HeaderInfo.java    From dataflow-java with Apache License 2.0 5 votes vote down vote up 
public static HeaderInfo getHeaderFromBAMFile(Storage.Objects storage, String BAMPath, Iterable<Contig> explicitlyRequestedContigs) throws IOException {
  HeaderInfo result = null;

  // Open and read start of BAM
  LOG.info("Reading header from " + BAMPath);
  final SamReader samReader = BAMIO
      .openBAM(storage, BAMPath, ValidationStringency.DEFAULT_STRINGENCY);
  final SAMFileHeader header = samReader.getFileHeader();
  Contig firstContig = getFirstExplicitContigOrNull(header, explicitlyRequestedContigs);
  if (firstContig == null) {
    final SAMSequenceRecord seqRecord = header.getSequence(0);
    firstContig = new Contig(seqRecord.getSequenceName(), -1, -1);
  }

  LOG.info("Reading first chunk of reads from " + BAMPath);
  final SAMRecordIterator recordIterator = samReader.query(
      firstContig.referenceName, (int)firstContig.start + 1, (int)firstContig.end + 1, false);

  Contig firstShard = null;
  while (recordIterator.hasNext() && result == null) {
    SAMRecord record = recordIterator.next();
    final int alignmentStart = record.getAlignmentStart();
    if (firstShard == null && alignmentStart > firstContig.start &&
        (alignmentStart < firstContig.end || firstContig.end == -1)) {
      firstShard = new Contig(firstContig.referenceName, alignmentStart, alignmentStart);
      LOG.info("Determined first shard to be " + firstShard);
      result = new HeaderInfo(header, firstShard);
    }
  }
  recordIterator.close();
  samReader.close();

  if (result == null) {
    throw new IOException("Did not find reads for the first contig " + firstContig.toString());
  }
  LOG.info("Finished header reading from " + BAMPath);
  return result;
}
Example 3
Source File: PSBwaUtils.java    From gatk with BSD 3-Clause "New" or "Revised" License 5 votes vote down vote up 
static void addReferenceSequencesToHeader(final SAMFileHeader header,
                                          final String referenceDictionaryPath) {
    final List<SAMSequenceRecord> refSeqs = getReferenceSequences(referenceDictionaryPath);
    for (final SAMSequenceRecord rec : refSeqs) {
        if (header.getSequence(rec.getSequenceName()) == null) {
            header.addSequence(rec);
        }
    }
}
Example 4
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;
}