Java Code Examples for htsjdk.samtools.SAMRecord#setHeader()

The following examples show how to use htsjdk.samtools.SAMRecord#setHeader() . 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: ReplaceSamHeader.java    From picard with MIT License 6 votes vote down vote up 
private void standardReheader(final SAMFileHeader replacementHeader) {
    final SamReader recordReader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).validationStringency(ValidationStringency.SILENT).open(INPUT);
    if (replacementHeader.getSortOrder() != recordReader.getFileHeader().getSortOrder()) {
        throw new PicardException("Sort orders of INPUT (" + recordReader.getFileHeader().getSortOrder().name() +
                ") and HEADER (" + replacementHeader.getSortOrder().name() + ") do not agree.");
    }
    final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(replacementHeader, true, OUTPUT);

    final ProgressLogger progress = new ProgressLogger(Log.getInstance(ReplaceSamHeader.class));
    for (final SAMRecord rec : recordReader) {
        rec.setHeader(replacementHeader);
        writer.addAlignment(rec);
        progress.record(rec);
    }
    writer.close();
    CloserUtil.close(recordReader);
}
Example 2
Source File: SamBamUtils.java    From chipster with MIT License 5 votes vote down vote up 
public void normaliseBam(File bamFile, File normalisedBamFile) {

		// Read in a BAM file and its header
		SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
		SAMFileReader reader = new SAMFileReader(IOUtil.openFileForReading(bamFile));
		SAMFileWriter writer = null;
		try {
			SAMFileHeader normalisedHeader = reader.getFileHeader();

			// Alter the chromosome names in header's SAMSequenceDictionary
			SAMSequenceDictionary normalisedDictionary = new SAMSequenceDictionary();
			for (SAMSequenceRecord sequenceRecord : normalisedHeader.getSequenceDictionary().getSequences()) {

				// Normalise chromosome
				String sequenceName = chromosomeNormaliser.normaliseChromosome(sequenceRecord.getSequenceName());
				normalisedDictionary.addSequence(new SAMSequenceRecord(sequenceName, sequenceRecord.getSequenceLength()));
			}
			normalisedHeader.setSequenceDictionary(normalisedDictionary);

			// Write new BAM file with normalised chromosome names
			writer = new SAMFileWriterFactory().makeBAMWriter(normalisedHeader, true, normalisedBamFile);
			for (final SAMRecord rec : reader) {
				rec.setHeader(normalisedHeader);
				writer.addAlignment(rec);
			}
			
		} finally {
			closeIfPossible(reader);
			closeIfPossible(writer);
		}
	}
Example 3
Source File: ReorderSam.java    From picard with MIT License 4 votes vote down vote up 
/**
 * Helper function that writes reads from iterator it into writer out, updating each SAMRecord along the way
 * according to the newOrder mapping from dictionary index -> index.  Name is used for printing only.
 */
private void writeReads(final SAMFileWriter out,
                        final SAMRecordIterator it,
                        final Map<Integer, Integer> newOrder,
                        final String name) {
    long counter = 0;
    log.info("  Processing " + name);

    while (it.hasNext()) {
        counter++;
        final SAMRecord read = it.next();
        final int oldRefIndex = read.getReferenceIndex();
        final int oldMateIndex = read.getMateReferenceIndex();
        final int newRefIndex = newOrderIndex(read, oldRefIndex, newOrder);

        read.setHeader(out.getFileHeader());
        read.setReferenceIndex(newRefIndex);

        // read becoming unmapped
        if (oldRefIndex != NO_ALIGNMENT_REFERENCE_INDEX &&
                newRefIndex == NO_ALIGNMENT_REFERENCE_INDEX) {
            read.setAlignmentStart(NO_ALIGNMENT_START);
            read.setReadUnmappedFlag(true);
            read.setCigarString(SAMRecord.NO_ALIGNMENT_CIGAR);
            read.setMappingQuality(SAMRecord.NO_MAPPING_QUALITY);
        }

        final int newMateIndex = newOrderIndex(read, oldMateIndex, newOrder);
        if (oldMateIndex != NO_ALIGNMENT_REFERENCE_INDEX &&
                newMateIndex == NO_ALIGNMENT_REFERENCE_INDEX) { // mate becoming unmapped
            read.setMateAlignmentStart(NO_ALIGNMENT_START);
            read.setMateUnmappedFlag(true);
            read.setAttribute(SAMTag.MC.name(), null);      // Set the Mate Cigar String to null
        }
        read.setMateReferenceIndex(newMateIndex);

        out.addAlignment(read);
    }

    it.close();
    log.info("Wrote " + counter + " reads");
}
Example 4
Source File: SAMRecordWriter.java    From Hadoop-BAM with MIT License 4 votes vote down vote up 
protected void writeAlignment(final SAMRecord rec) {
	rec.setHeader(header);
	writer.writeAlignment(rec);
}