Java SAMFileWriterFactory.makeBAMWriter方法代码示例

import htsjdk.samtools.SAMFileWriterFactory; //导入方法依赖的package包/类
public void open(final SAMFileHeader src)
{
SAMFileWriterFactory samFileWriterFactory=writingBamArgs.createSAMFileWriterFactory();
samFileWriterFactory.setMaxRecordsInRam(writingSortingCollection.getMaxRecordsInRam());
samFileWriterFactory.setTempDirectory(writingSortingCollection.getTmpDirectories().get(0));


final File fileout=getFile();
LOG.info("opening BAM file "+fileout);
final File parent=fileout.getParentFile();
if(parent!=null) {
	parent.mkdirs();
	samFileWriterFactory.setTempDirectory(writingSortingCollection.getTmpDirectories().get(0));
}


this.header= src.clone();
this.header.addComment(
		"Processed with "+getProgramCommandLine()+
		" version:"+getVersion()+
		"CommandLine:"+getProgramCommandLine()
		);

this.header.setSortOrder(SortOrder.coordinate);
samFileWriterFactory.setCreateIndex(true);
	

this._writer = samFileWriterFactory.makeBAMWriter(
	this.header,
	true,
	fileout
	);
}
 

import htsjdk.samtools.SAMFileWriterFactory; //导入方法依赖的package包/类
public static void main(String[] args) throws IOException, ParseException {
	EvidenceRecordFileIterator iterator = new EvidenceRecordFileIterator(new File(args[0]));
	Read context = new Read();
	SAMFileHeader header = new SAMFileHeader();
	header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
	SAMSequenceRecord samSequenceRecord = new SAMSequenceRecord("chr10", 135534747);
	samSequenceRecord.setAttribute(SAMSequenceRecord.ASSEMBLY_TAG, iterator.assembly_ID);
	String readGroup = String.format("%s-%s", iterator.assembly_ID, iterator.chromosome);
	SAMReadGroupRecord readGroupRecord = new SAMReadGroupRecord(readGroup);
	readGroupRecord.setAttribute(SAMReadGroupRecord.READ_GROUP_SAMPLE_TAG, iterator.sample);
	readGroupRecord.setAttribute(SAMReadGroupRecord.PLATFORM_UNIT_TAG, readGroup);
	readGroupRecord.setAttribute(SAMReadGroupRecord.SEQUENCING_CENTER_TAG, "\"Complete Genomics\"");
	Date date = new SimpleDateFormat("yyyy-MMM-dd hh:mm:ss.S").parse(iterator.generatedAt);
	readGroupRecord.setAttribute(SAMReadGroupRecord.DATE_RUN_PRODUCED_TAG,
			new SimpleDateFormat("yyyy-MM-dd").format(date));
	readGroupRecord.setAttribute(SAMReadGroupRecord.PLATFORM_TAG, "\"Complete Genomics\"");
	header.addReadGroup(readGroupRecord);

	header.addSequence(samSequenceRecord);

	SAMFileWriterFactory f = new SAMFileWriterFactory();
	SAMFileWriter samWriter;
	if (args.length > 1)
		samWriter = f.makeBAMWriter(header, false, new File(args[1]));
	else
		samWriter = f.makeSAMWriter(header, false, System.out);
	int i = 0;
	long time = System.currentTimeMillis();
	DedupIterator dedupIt = new DedupIterator(iterator);

	while (dedupIt.hasNext()) {
		EvidenceRecord evidenceRecord = dedupIt.next();
		if (evidenceRecord == null)
			throw new RuntimeException();
		try {
			context.reset(evidenceRecord);
			context.parse();
		} catch (Exception e) {
			System.err.println("Failed on line:");
			System.err.println(evidenceRecord.line);
			throw new RuntimeException(e);
		}

		SAMRecord[] samRecords = context.toSAMRecord(header);
		for (SAMRecord samRecord : samRecords) {
			samRecord.setAttribute(SAMTag.RG.name(), readGroup);
			samWriter.addAlignment(samRecord);
		}

		i++;
		if (i % 1000 == 0) {
			if (System.currentTimeMillis() - time > 10 * 1000) {
				time = System.currentTimeMillis();
				System.err.println(i);
			}
		}

		if (i > 10000)
			break;
	}
	samWriter.close();
}
 

import htsjdk.samtools.SAMFileWriterFactory; //导入方法依赖的package包/类
public static void main(String[] args) throws IOException {
	Params params = new Params();
	JCommander jc = new JCommander(params);
	jc.parse(args);

	Log.setGlobalLogLevel(params.logLevel);

	if (args.length == 0 || params.help) {
		usage(jc);
		System.exit(1);
	}

	if (params.reference == null) {
		System.out.println("Reference file not found, will try downloading...");
	}

	ReferenceSource referenceSource = null;
	if (params.reference != null) {
		System.setProperty("reference", params.reference.getAbsolutePath());
		referenceSource = new ReferenceSource(params.reference);
	} else {
		String prop = System.getProperty("reference");
		if (prop != null) {
			referenceSource = new ReferenceSource(new File(prop));
		}
	}

	SamReaderFactory factory = SamReaderFactory.make().validationStringency(params.validationLevel);
	SamInputResource r;
	if ("file".equalsIgnoreCase(params.url.getProtocol()))
		r = SamInputResource.of(params.url.getPath());
	else
		r = SamInputResource.of(params.url);
	SamReader reader = factory.open(r);
	SAMRecordIterator iterator = reader.iterator();

	SAMFileWriterFactory writerFactory = new SAMFileWriterFactory();
	SAMFileWriter writer = null;
	OutputStream os = new BufferedOutputStream(new FileOutputStream(params.outputFile));
	switch (params.outputFormat) {
	case BAM:
		writer = writerFactory.makeBAMWriter(reader.getFileHeader(),
				reader.getFileHeader().getSortOrder() == SortOrder.coordinate, os);
		break;
	case CRAM:
		writer = writerFactory.makeCRAMWriter(reader.getFileHeader(), os, params.reference);
		break;

	default:
		System.out.println("Unknown output format: " + params.outputFormat);
		System.exit(1);
	}

	while (iterator.hasNext()) {
		writer.addAlignment(iterator.next());
	}
	writer.close();
	reader.close();
}
 

import htsjdk.samtools.SAMFileWriterFactory; //导入方法依赖的package包/类
public static void main(String[] args) throws IOException {
//		Logger.LEVEL = Logger.Level.TRACE;
		String ref = "/home/lmose/dev/reference/hg38b/hg38.fa";
		
		CompareToReference2 c2r = new CompareToReference2();
		c2r.init(ref);
		
		ChromosomeChunker cc = new ChromosomeChunker(c2r);
		
		cc.init();
		
//		SamReader reader = SAMRecordUtils.getSamReader("/home/lmose/dev/abra2_dev/sort_issue3/0.5.bam");
//		SamReader reader = SAMRecordUtils.getSamReader("/home/lmose/dev/abra2_dev/sort_issue4/1.6.bam");
		SamReader reader = SAMRecordUtils.getSamReader("/home/lmose/dev/abra2_dev/mate_fix/0.87.bam");

		SAMFileHeader header = reader.getFileHeader();
		header.setSortOrder(SortOrder.coordinate);
		
		int maxRecordsInRam = 1000000;
		SAMRecord[] readsByNameArray = new SAMRecord[maxRecordsInRam];
		SAMRecord[] readsByCoordArray = new SAMRecord[maxRecordsInRam];
		
		SortedSAMWriter writer = new SortedSAMWriter(new String[] { "/home/lmose/dev/abra2_dev/mate_fix" }, "/home/lmose/dev/abra2_dev/mate_fix", new SAMFileHeader[] { reader.getFileHeader() }, true, cc,
				1,true,1000,false, false, false, maxRecordsInRam);

		SAMFileWriterFactory writerFactory = new SAMFileWriterFactory();
		SAMFileWriter out = writerFactory.makeBAMWriter(reader.getFileHeader(), true, new File("/home/lmose/dev/abra2_dev/mate_fix/test.bam"),1);
		
		long start = System.currentTimeMillis();
		
		writer.processChromosome(out, 0, "chr12", readsByNameArray, readsByCoordArray);
		
		out.close();
		
		long stop = System.currentTimeMillis();
		
		System.out.println("Elapsed msecs: " + (stop-start));
	}