Java SAMRecord.getReferenceName方法代码示例

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
/**
 * Converts a SAM record into a bed entry and outputs it straight away
 *
 * @param record
 */
private void processOneUnalignedRecord(SAMRecord record) {

    // output the alignment positions into a bed file
    int start = record.getAlignmentStart() - 1;
    int end = start + record.getReadLength();
    String out = record.getReferenceName() + "\t" + start + "\t" + end + "\n";

    synchronized (outunaligned) {
        try {
            outunaligned.write(out.getBytes());
        } catch (Exception ex) {
            System.out.println("Exception writing unaligned bed: " + ex.getMessage());
        }
    }

    // create a dummy thesaurus entry
    ThesaurusEntry entry = new ThesaurusEntry(record, ginfo);
    // complete it (need to fix alignment end manually, then use function to get anchors set right)
    entry.alignEnd = entry.originEnd;
    completeThesaurusEntry(entry, record);
    // set the origin chromosome to -1 to signal unaligned setup
    entry.originChrIndex = -1;
    outputThesaurusEntry(entry, outstreams.get(entry.getAlignChr()));

}
 

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
/**
 * copy reads from one bam file and put them into files by chromosome.
 *
 * @param nowbam
 */
private void splitIntoChroms(File nowbam) {
    SAMFileReader inputSam = new SAMFileReader(nowbam);

    // write each aligned record into its separate file, or into "unmapped"
    for (final SAMRecord record : inputSam) {
        String nowchrom = record.getReferenceName();
        SAMFileWriter nowwriter = chrombams.get(nowchrom);
        if (nowwriter == null) {
            nowwriter = chrombams.get("unmapped");
        }
        nowwriter.addAlignment(record);
    }

    inputSam.close();
}
 

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
public SequenceRead(SAMRecord record) {
    super(record.getAlignmentStart(), record.getAlignmentEnd());
    this.chr = record.getReferenceName();
    if (record.getReadNegativeStrandFlag()) {
        strand = Strand.NEGATIVE;
    } else {
        strand = Strand.POSITIVE;
    }
    this.readBases = record.getReadBases();
    this.qualities = record.getBaseQualities();
    this.alignmentBlocks = record.getAlignmentBlocks();
}
 

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
public static SAMRecord convertToPairedEndFragment(SAMRecord rec) {
	int insertSize = Math.abs(rec.getInferredInsertSize());
	//TODO: possible to remove (insertSize > 0) clause? What does an insert size of 0 mean?
	if (rec.getReadPairedFlag() && rec.getProperPairFlag() && !rec.getReadUnmappedFlag() 
			&& (insertSize <= MAX_INSERT) && (rec.getAlignmentStart() < rec.getMateAlignmentStart())
			&& rec.getReferenceName() != "chrM") // current paired end representation doesn't do well with circular chromosomes
	{
		//We need to get the full fragment contained by read.getStart to pair.getEnd
		int readEnd=rec.getAlignmentEnd();
		int mateStart=rec.getMateAlignmentStart();
					
		//int extension = insertSize - rec.getReadLength();
		int extension=(mateStart-readEnd)+rec.getReadLength();
		if (extension <= MAX_INSERT) {
			String newRead = rec.getReadString() + StringUtils.repeat("N", extension);
			rec.setReadString(newRead);
			String newQual = StringUtils.repeat("A", newRead.length());
			if(!rec.getBaseQualityString().equals("*")) newQual = rec.getBaseQualityString() + StringUtils.repeat("A", extension);
			rec.setBaseQualityString(newQual);
			String newCigar=newRead.length()+"M";
			rec.setCigarString(newCigar);

			// Change attributes to represent single read
			rec.setMateReferenceName("*");
			rec.setMateAlignmentStart(0);
			rec.setFirstOfPairFlag(false);
			rec.setMateNegativeStrandFlag(false);
			rec.setMateUnmappedFlag(false);
			rec.setProperPairFlag(false);
			rec.setReadPairedFlag(false);
			rec.setSecondOfPairFlag(false);
		}
	} else {
		rec = null;
	}
	return rec;
}
 

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
public static Gene SAMFormatFullBED(SAMRecord sam){
	String chr=sam.getReferenceName();
   	int start=sam.getAlignmentStart()-1; //TODO: Do we need the -1, it is a left over from the method above.
   	Strand strand=sam.getReadNegativeStrandFlag() ? Strand.NEGATIVE : Strand.POSITIVE;
   	String cigar= sam.getCigarString(); //parse cigar and put the breaks into their component parts, in parallel keep track of the splices
   	Collection<Alignments> aligns=parseCigar(cigar, chr, start);
	Gene gene=new Gene( aligns);
	gene.setName(sam.getReadName());
	gene.setOrientation(strand);
	if(sam.getReadString() != null) {gene.setSequence(sam.getReadString()); }
   	return gene;
}
 

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
public SingleEndAlignment(SAMRecord read) {
  	super(read.getReferenceName(), read.getAlignmentStart()-1, read.getAlignmentStart()); //This is a dummy setup
  	parseCigar(read.getCigarString(), read.getReferenceName(), read.getAlignmentStart()-1);
  	long startT = System.nanoTime();
  	setName(read.getReadName());
long cTime = System.nanoTime() - startT;
cTime = Math.round(cTime/(double)1000000);
if(cTime > 50) {
	logger.debug("parse set read name  took " + cTime);
}

startT = System.nanoTime();
  	if (read.getReadNegativeStrandFlag()) 
  		setOrientation(Strand.NEGATIVE);
  	else
  		setOrientation(Strand.POSITIVE);
cTime = System.nanoTime() - startT;
cTime = Math.round(cTime/(double)1000000);
if(cTime > 50) {
	logger.debug("Set orientation took " + cTime);
}

  	startT = System.nanoTime();
  	try {
  		record = (SAMRecord) read.clone();
  	} catch (CloneNotSupportedException e) {
  		logger.warn("Caught exception on record " + read.getReadName());
  		e.printStackTrace();
  	}
  	//record=new WrapSamRecord(read);
  	assert(read.getAlignmentEnd() == getEnd()); // sanity check
cTime = System.nanoTime() - startT;
cTime = Math.round(cTime/(double)1000000);
if(cTime > 50) {
	logger.debug("Cloning object took " + cTime);
}
  }
 

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
private boolean isCompatiblePair(SAMRecord r1, SAMRecord r2) {
	if(r1.getReferenceName()==r2.getReferenceName()){
		if((r1.getAlignmentStart()==r2.getMateAlignmentStart())&& (r1.getMateAlignmentStart()==r2.getAlignmentStart())){
			if(r1.getMateNegativeStrandFlag()==r2.getReadNegativeStrandFlag() && r1.getReadNegativeStrandFlag()==r2.getMateNegativeStrandFlag()){
				if(r1.getMateReferenceName().equalsIgnoreCase(r2.getReferenceName()) && r2.getMateReferenceName().equalsIgnoreCase(r1.getReferenceName())){
					return true;
				}
			}
		}
	}
	return false;
}
 

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
/**
 * Get sam line for record
 * @param rec The record
 * @return Sam formatted line ending in newline
 */
public static String getSamString(SAMRecord rec) {
	
	// Make string representation of record in sam format
	String rtrn = rec.getReadName() + "\t";
	
	// Get sam flags
	int flags = 0;
	// 0x1 template having multiple segments in sequencing
	if(rec.getReadPairedFlag()) flags += 1;
	// 0x4 segment unmapped
	if(rec.getReadUnmappedFlag()) flags += 4;
	// 0x10 SEQ being reverse complemented
	if(rec.getReadNegativeStrandFlag()) flags += 16;
	// 0x100 secondary alignment
	if(rec.getNotPrimaryAlignmentFlag()) flags += 256;
	// 0x200 not passing quality controls
	if(rec.getReadFailsVendorQualityCheckFlag()) flags += 512;
	// 0x400 PCR or optical duplicate
	if(rec.getDuplicateReadFlag()) flags += 1024;
	
	if(rec.getReadPairedFlag()) {
		// 0x2 each segment properly aligned according to the aligner
		if(rec.getProperPairFlag()) flags += 2;
		// 0x8 next segment in the template unmapped
		if(rec.getMateUnmappedFlag()) flags += 8;
		// 0x20 SEQ of the next segment in the template being reversed
		if(rec.getMateNegativeStrandFlag()) flags += 32;
		// 0x40 the first segment in the template
		if(rec.getFirstOfPairFlag()) flags += 64;
		// 0x80 the last segment in the template
		if(rec.getSecondOfPairFlag()) flags += 128;
	}
	
	rtrn += Integer.valueOf(flags).toString() + "\t";
	
	// The rest of the sam fields
	rtrn += rec.getReferenceName() + "\t";
	rtrn += rec.getAlignmentStart() + "\t";
	rtrn += rec.getMappingQuality() + "\t";
	rtrn += rec.getCigarString() + "\t";
	rtrn += rec.getMateReferenceName() + "\t";
	rtrn += rec.getMateAlignmentStart() + "\t";
	rtrn += rec.getInferredInsertSize() + "\t";
	rtrn += rec.getReadString() + "\t";
	rtrn += rec.getBaseQualityString() + "\n";
	
	return rtrn;
}