本文整理汇总了Java中net.sf.samtools.SAMRecord.setReadBases方法的典型用法代码示例。如果您正苦于以下问题：Java SAMRecord.setReadBases方法的具体用法？Java SAMRecord.setReadBases怎么用？Java SAMRecord.setReadBases使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类net.sf.samtools.SAMRecord的用法示例。
在下文中一共展示了SAMRecord.setReadBases方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: testAlignmentOfRecord
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));
}
示例2: createSAMRecord
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;
}
示例3: getSAMRecord
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;
}