Java SAMRecord.setReferenceName方法代码示例

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
/**
 * 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 void main (String [] args) throws IOException {
	ArgumentMap argMap = CLUtil.getParameters(args,USAGE , "default");
	String alnFile = argMap.getInput();
	String out = argMap.getOutput();
	List<String> seqsToChange = new ArrayList<String>();
	if(argMap.containsKey("seqsToFix")) {
		seqsToChange = CLUtil.listFromArray(argMap.getMandatory("seqsToFix").split(","));
	}

	SAMFileReader reader = new SAMFileReader(new File(alnFile));
	SAMFileWriterFactory samfwf = new SAMFileWriterFactory();
	SAMFileHeader oldHeader = reader.getFileHeader();
	SAMFileHeader header = oldHeader.clone();
	header.setSortOrder(oldHeader.getSortOrder());
	oldHeader.getAttributes();
	for (Map.Entry<String, String> he : oldHeader.getAttributes()) { 
		header.setAttribute(he.getKey(), he.getValue());
	}
	
	
	
	header.addProgramRecord(new SAMProgramRecord("nextgen.core.programs.FixChromosomeNames -in " + alnFile + " -out " + out));
	SAMSequenceDictionary ssd = header.getSequenceDictionary();
	SAMSequenceDictionary newSSD = new SAMSequenceDictionary();
	List<SAMSequenceRecord > sequences = ssd.getSequences();
	for (SAMSequenceRecord s : sequences) {
		if(seqsToChange.isEmpty() || seqsToChange.contains(s.getSequenceName())) {
			SAMSequenceRecord ns = new SAMSequenceRecord("chr" + s.getSequenceName(), s.getSequenceLength());
			ns.setAssembly(s.getAssembly());
			ns.setSpecies(ns.getSpecies());
			for (Map.Entry<String, String> e : s.getAttributes()) { 
				ns.setAttribute(e.getKey(), e.getValue());
			}
			newSSD.addSequence(ns);
		} else {
			newSSD.addSequence(s);
		}
	}
	header.setSequenceDictionary(newSSD);
	
	samfwf.setCreateIndex(true);
	SAMFileWriter writer = samfwf.makeBAMWriter(header, true, new File(out))  ;
	
	Iterator<SAMRecord> alnIt = reader.iterator();
	while (alnIt.hasNext()) {
		SAMRecord a = alnIt.next();
		if(seqsToChange.isEmpty() || seqsToChange.contains(a.getReferenceName())) {
			a.setReferenceName("chr"+a.getReferenceName());
			a.setHeader(header);
		}
		writer.addAlignment(a);
	}
	
	reader.close();
	writer.close();

}