Java SAMRecord.setCigarString方法代码示例

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
private SAMRecord createSAMRecord(String read, String cigar, String md, int NM, boolean reverse) {
	SAMFileHeader header = new SAMFileHeader();
	List<SAMProgramRecord> PRs = new ArrayList<>();
	PRs.add(new SAMProgramRecord("Bowtie"));
	header.setProgramRecords(PRs);

	SAMRecord record = new SAMRecord(header);
	record.setReadString(read);
	record.setAttribute("NM", NM); //number of mismatches
	record.setCigarString(cigar);
	record.setAttribute("MD", md);

	if (reverse) {
		record.setReadNegativeStrandFlag(true);
	}

	return record;
}
 

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
@Test
public void testAlignmentOfRecord() throws Exception {
    SAMRecord record = new SAMRecord(this.header);
    record.setReadBases("TCCGTTAGTC".getBytes());
    record.setReadName(queryName);
    record.setCigarString("1S3M1I4M1S");
    record.setReferenceIndex(0);
    record.setReferenceName(this.referenceName);
    record.setAlignmentStart(2);

    assertEquals(referenceName, record.getReferenceName());

    Alignment result = SAMBEASTUtils.alignmentOfRecord(record, this.reference);
    assertEquals(2, result.getTaxonCount());
    assertEquals(new String(reference), result.getAlignedSequenceString(0));
    assertEquals("-CCGTAGT-", result.getAlignedSequenceString(1));
    assertEquals(referenceName, result.getTaxonId(0));
    assertEquals(queryName, result.getTaxonId(1));
}
 

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
@Override
public final SAMRecord toSAMRecord() {
	SAMRecord record = firstMate.toSAMRecord();
	
	record.setAttribute(PairedEndWriter.readStartFlag, Integer.valueOf(firstMate.getSAMStart()));
	record.setAttribute(PairedEndWriter.readCigarFlag, firstMate.getCigarString());
	record.setAttribute(PairedEndWriter.mateSequenceFlag, secondMate.getReadSequence());
	record.setAttribute(PairedEndWriter.mateCigarFlag, secondMate.getCigarString());
	
	record.setMateAlignmentStart(secondMate.getSAMStart());
	// add by @zhuxp
       record.setAlignmentStart(this.getAlignmentStart()+1);
    
	// end of add (test version)
       
       Annotation fragment = getReadAlignmentBlocks(null);
	record.setCigarString(fragment.getLengthOnReference() + "M");  // NOTE: losing information about indels in the SingleEndAlignments	
	record.setInferredInsertSize(fragment.getLengthOnReference());

	return record;
}
 

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
/**
 * Converts a blat psl entry into a SAM record.
 *
 * @param entry
 * @param bases
 * @param hh
 * @param ns
 *
 * number of blat entries with the same score
 *
 * @param sd
 *
 * rank-dependent interpretation. For first rank, distance to next best
 * match. For other ranks distance from first match.
 *
 * @param bs
 *
 * number of matches in best score
 *
 * @param matchrankA
 *
 * rank of this blat entry in a sorted list of entries (low rank means
 * better alignment, modulo equal matching entries)
 *
 * @param matchrankB
 *
 * alternative rank (optimistic/pessimistic rank)
 *
 * @param readgroup
 *
 * @return
 */
private SAMRecord createSAMRecord(PslEntry entry, String bases, SAMFileHeader hh,
        int ns, int sd, int bs, int matchrankA, int matchrankB, String readgroup) {

    //System.out.println("in create pair");

    SAMRecord sr = new SAMRecord(hh);

    // set flags for a neutral read
    sr.setFlags(0);
    sr.setAlignmentStart(entry.Tstart + 1);
    sr.setMateAlignmentStart(entry.Tstart + 1);
    sr.setCigarString(entry.makeCigar());
    sr.setReferenceName(entry.Tname);
    sr.setReadName(entry.Qname);
    sr.setMappingQuality(Math.min(254, entry.match));
    if (entry.strand == '-') {
        sr.setReadNegativeStrandFlag(true);
        sr.setReadBases(SequenceComplementer.complement(bases.getBytes()));
    } else {
        sr.setReadNegativeStrandFlag(false);
        sr.setReadBases(bases.getBytes());
    }
    sr.setBaseQualityString(makeBaseQuality(bases.length()));
    sr.setAttribute("ns", ns);
    sr.setAttribute("sd", sd);
    sr.setAttribute("bs", bs);
    sr.setAttribute("ra", matchrankA);
    sr.setAttribute("rb", matchrankB);
    sr.setAttribute("RG", readgroup);

    return sr;
}
 

import net.sf.samtools.SAMRecord; //导入方法依赖的package包/类
public SAMRecord getSAMRecord(SAMFileHeader hh) {
    SAMRecord sr = new SAMRecord(hh);

    // set flags for a neutral read
    sr.setFlags(0);
    sr.setReadName(getReadname());
    sr.setBaseQualityString(makeBaseQuality(readsequence.length));
    sr.setAttribute("RG", "thesalign");
    sr.setNotPrimaryAlignmentFlag(!isPrimary());
    sr.setAlignmentStart(alignpos + 1);
    sr.setCigarString(readsequence.length + "M");
    sr.setReferenceName(chrom);
    sr.setMappingQuality(mappingquality);
    if (negativestrand) {
        sr.setReadNegativeStrandFlag(true);
        sr.setReadBases(SequenceComplementer.complement(readsequence));
    } else {
        sr.setReadNegativeStrandFlag(false);
        sr.setReadBases(readsequence);
    }

    // perhaps the read is unaligned (too many alignments to report)
    if (unmapped) {
        sr.setReadUnmappedFlag(unmapped);
    }

    return sr;
}
 

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;
}