Java Code Examples for htsjdk.samtools.SAMFileReader#setDefaultValidationStringency()

public static void sortSamBam(File samBamFile, File sortedBamFile) {
	
	SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
	SAMFileReader reader = new SAMFileReader(IOUtil.openFileForReading(samBamFile));
	SAMFileWriter writer = null;
	try {
		
		reader.getFileHeader().setSortOrder(SAMFileHeader.SortOrder.coordinate);
		writer = new SAMFileWriterFactory().makeBAMWriter(reader.getFileHeader(), false, sortedBamFile);
		Iterator<SAMRecord> iterator = reader.iterator();
		while (iterator.hasNext()) {
			writer.addAlignment(iterator.next());
		}
		
	} finally {
		closeIfPossible(reader);
		closeIfPossible(writer);
	}
}
 

public void indexBam(File bamFile, File baiFile) {
	SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
       final SamReader bam;

           // input from a normal file
           IOUtil.assertFileIsReadable(bamFile);
           bam = SamReaderFactory.makeDefault().referenceSequence(null)
                   .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS)
                   .open(bamFile);

       if (bam.type() != SamReader.Type.BAM_TYPE) {
           throw new SAMException("Input file must be bam file, not sam file.");
       }

       if (!bam.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate)) {
           throw new SAMException("Input bam file must be sorted by coordinate");
       }

       BAMIndexer.createIndex(bam, baiFile);

       CloserUtil.close(bam);
}
 

public String printSamBam(InputStream samBamStream, int maxRecords) throws IOException {
	SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
	SAMFileReader in = new SAMFileReader(samBamStream);
	SAMFileHeader header = in.getFileHeader();
	ByteArrayOutputStream buffer = new ByteArrayOutputStream();
	SAMFileWriter out = new SAMFileWriterFactory().makeSAMWriter(header, true, buffer);
	int i = 0;
	try {
		for (final SAMRecord rec : in) {
			if (i > maxRecords) {
				break;
			}
			out.addAlignment(rec);
			i++;
		}
	} finally {
		closeIfPossible(out);
	}

	if (i > maxRecords) {
		buffer.write("SAM/BAM too long for viewing, truncated here!\n".getBytes());
	}
	
	return buffer.toString();
}
 

/**
  * Generally we would like to have both data and index files,
  * because otherwise we cannot access random locations.
  * 
  * @param data
  * @param index
  * @throws URISyntaxException
  * @throws IOException 
  */
 public BamDataSource(DataUrl data, DataUrl index) throws URISyntaxException, IOException {
     super(data);

 	// BAMFileReader emits useless warning to System.err that can't be turned off,
 	// so we direct it to other stream and discard. 
 	PrintStream originalErr = System.err;
 	System.setErr(new PrintStream(new ByteArrayOutputStream()));
 	
 	SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
 	this.reader = SamBamUtils.getSAMReader(data.getUrl(), index.getUrl());

 	LinkedList<String> chrList = new LinkedList<>();
 	
 	// Iterate chromosomes to check naming convention
 	for (SAMSequenceRecord sequenceRecord : this.reader.getFileHeader().getSequenceDictionary().getSequences()) {
 		
 		String name = sequenceRecord.getSequenceName();
 		
chrList.add(name);
 	}
 	
 	// Create unnormaliser for this naming convention
 	// Look only at the first sequence (assume all have the same convention)
 	this.chromosomeNameUnnormaliser = new ChromosomeNameUnnormaliser(chrList);      
     
     // Restore System.err
     System.setErr(originalErr);
 }
 

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);
		}
	}
 

@Override
public void doRun() throws IOException {
	super.doRun();

	fo.close();

	if (fo.empty)
		return;

	log.info("Sorting overflow BAM: ", fo.file.length());
	SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
	SAMFileReader r = new SAMFileReader(fo.file);
	SAMRecordIterator iterator = r.iterator();
	if (!iterator.hasNext()) {
		r.close();
		fo.file.delete();
		return;
	}

	SAMRecord r1 = iterator.next();
	SAMRecord r2 = null;
	counter = multiFastqOutputter.getCounter();
	log.info("Counter=" + counter);
	while (!brokenPipe.get() && iterator.hasNext()) {
		r2 = iterator.next();
		if (r1.getReadName().equals(r2.getReadName())) {
			print(r1, r2);
			counter++;
			r1 = null;
			if (!iterator.hasNext())
				break;
			r1 = iterator.next();
			r2 = null;
		} else {
			print(r1, 0);
			r1 = r2;
			r2 = null;
			counter++;
		}
	}
	if (r1 != null)
		print(r1, 0);
	r.close();
	fo.file.delete();
}
 

@Test
public void test() throws IOException {
	byte[] buf = new byte[1024];
	BAMRecordView view = new BAMRecordView(buf);
	view.setRefID(0);
	view.setAlignmentStart(77);
	view.setMappingScore(44);
	view.setIndexBin(99);
	view.setFlags(555);
	view.setMateRefID(0);
	view.setMateAlStart(78);
	view.setInsertSize(133);

	view.setReadName("name1");
	view.setCigar(TextCigarCodec.decode("10M"));
	view.setBases("AAAAAAAAAA".getBytes());
	view.setQualityScores("BBBBBBBBBB".getBytes());

	int id = 'A' << 16 | 'M' << 8 | 'A';
	view.addTag(id, "Q".getBytes(), 0, 1);

	int len = view.finish();

	System.out.println(Arrays.toString(Arrays.copyOf(buf, len)));

	ByteArrayOutputStream baos = new ByteArrayOutputStream();

	SAMFileHeader header = new SAMFileHeader();
	header.addSequence(new SAMSequenceRecord("14", 14));

	ByteArrayOutputStream baos2 = new ByteArrayOutputStream();
	SAMFileWriter writer = new SAMFileWriterFactory().makeBAMWriter(header, true, baos2);
	SAMRecord record = new SAMRecord(header);
	record.setReferenceIndex(0);
	record.setAlignmentStart(1);
	record.setCigarString("10M");
	record.setFlags(555);
	record.setMappingQuality(44);
	record.setMateReferenceIndex(0);
	record.setMateAlignmentStart(0);
	record.setInferredInsertSize(133);
	record.setReadName("name1");
	record.setReadBases("AAAAAAAAAA".getBytes());
	record.setBaseQualities("BBBBBBBBBB".getBytes());
	record.setAttribute("AM", 'Q');

	System.out.println("BAMFileWriter.addAlignment():");
	writer.addAlignment(record);
	System.out.println(".");
	writer.close();

	System.out.println("------------------------------------------");
	System.out.println();
	System.out.println(new String(baos2.toByteArray()));
	System.out.println();

	SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
	SAMFileReader reader2 = new SAMFileReader(new ByteArrayInputStream(baos2.toByteArray()));
	SAMRecordIterator iterator = reader2.iterator();
	while (iterator.hasNext()) {
		record = iterator.next();
		System.out.println(record.getSAMString());
	}
	System.out.println("------------------------------------------");

	BlockCompressedOutputStream bcos = new BlockCompressedOutputStream(baos, null);
	bcos.write("BAM\1".getBytes());
	bcos.write(toByteArray(header));
	CramInt.writeInt32(header.getSequenceDictionary().size(), bcos);
	for (final SAMSequenceRecord sequenceRecord : header.getSequenceDictionary().getSequences()) {
		byte[] bytes = sequenceRecord.getSequenceName().getBytes();
		CramInt.writeInt32(bytes.length + 1, bcos);
		bcos.write(sequenceRecord.getSequenceName().getBytes());
		bcos.write(0);
		CramInt.writeInt32(sequenceRecord.getSequenceLength(), bcos);
	}
	bcos.write(buf, 0, len);
	bcos.close();

	System.out.println(new String(baos.toByteArray()));

	SAMFileReader reader = new SAMFileReader(new ByteArrayInputStream(baos.toByteArray()));
	iterator = reader.iterator();
	while (iterator.hasNext()) {
		record = iterator.next();
		System.out.println(record.getSAMString());
	}
	reader.close();

}