本文整理汇总了Java中htsjdk.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htsjdk.samtools.SAMRecord的用法示例。
在下文中一共展示了SAMRecord.setReadBases方法的1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: transfer
import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
public SAMRecord transfer(final BasicSamRecord basicSamRecord) {
final SAMRecord samRecord =
samRecordFactory.createSAMRecord(this.mFileHeader);
samRecord.setValidationStringency(this.validationStringency);
samRecord.setHeader(this.mFileHeader);
samRecord.setReadName(basicSamRecord.readName());
samRecord.setFlags(basicSamRecord.flag());
if (!basicSamRecord.contigName().equals("*")) {
samRecord.setReferenceName(basicSamRecord.contigName());
}
samRecord.setAlignmentStart(basicSamRecord.position());
samRecord.setMappingQuality(basicSamRecord.mapQ());
samRecord.setCigarString(basicSamRecord.cigar());
if (basicSamRecord.contigId() != FAKE_CONTIG_ID) {
samRecord.setMateReferenceName(basicSamRecord.mateContigName());
samRecord.setMateAlignmentStart(basicSamRecord.matePosition());
samRecord.setInferredInsertSize(basicSamRecord.infferdSize());
}
byte[] quality = null;
if (basicSamRecord.quality().length == 1 && basicSamRecord.quality()[0] == '*') {
samRecord.setBaseQualities(SAMRecord.NULL_QUALS);
} else {
quality = basicSamRecord.quality();
if (basicSamRecord.compressFlag()) {
quality = QualityCompressTools.deCompressQual(quality);
}
}
byte[] sequence = null;
if (basicSamRecord.sequence().length == 1 && basicSamRecord.sequence()[0] == '*') {
samRecord.setReadBases(SAMRecord.NULL_SEQUENCE);
} else {
sequence = basicSamRecord.sequence();
if (basicSamRecord.compressFlag()) {
sequence = BaseCompressTools.decompressBase(sequence, quality);
}
// 必须在执行之后解压之后再赋值，因为解压可能会导致quality变化。
samRecord.setBaseQualityString(new String(quality));
samRecord.setReadString(new String(sequence));
}
List<String> tmp = CollectionConverter.asJavaList(basicSamRecord.attributeList());
for (String attribute : tmp) {
parseTag(samRecord, attribute);
}
return samRecord;
}