本文整理汇总了Java中htsjdk.samtools.SAMRecord.getAttributes方法的典型用法代码示例。如果您正苦于以下问题：Java SAMRecord.getAttributes方法的具体用法？Java SAMRecord.getAttributes怎么用？Java SAMRecord.getAttributes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.getAttributes方法的2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
/**
* Write the record.
*
* @param alignment SAMRecord.
*/
public BasicSamRecord transfer(final SAMRecord alignment) {
String readName = alignment.getReadName();
int flags = alignment.getFlags();
int contigId = alignment.getReferenceIndex();
if (contigId == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
contigId = FAKE_CONTIG_ID;
}
String contigName = alignment.getReferenceName();
int position = alignment.getAlignmentStart();
int mapQ = alignment.getMappingQuality();
String cigar = alignment.getCigarString();
int mateContigId = alignment.getMateReferenceIndex();
if (mateContigId == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
mateContigId = FAKE_CONTIG_ID;
}
String mateContigName = alignment.getMateReferenceName();
int matePosition = alignment.getMateAlignmentStart();
int inferredSize = alignment.getInferredInsertSize();
byte[] sequence = alignment.getReadString().getBytes();
byte[] quality = alignment.getBaseQualityString().getBytes();
List<SAMRecord.SAMTagAndValue> attributes = alignment.getAttributes();
List<String> encodedTags = new ArrayList<>(attributes.size());
for (SAMRecord.SAMTagAndValue attribute : attributes) {
encodedTags.add(tagCodec.encode(attribute.tag, attribute.value));
}
// 在这里统一不压缩，压缩操作是由scala代码中的执行引擎统一调配的。
return BasicSamRecord.apply(false, readName, flags, contigId, contigName, position, mapQ,
cigar, mateContigId, mateContigName, matePosition, inferredSize,
sequence, quality, encodedTags);
}
示例2: GATKSAMRecord
import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
/**
* HACK TO CREATE GATKSAMRECORD BASED ONLY A SAMRECORD FOR TESTING PURPOSES ONLY
* @param read
*/
public GATKSAMRecord(final SAMRecord read) {
super(read.getHeader());
setReferenceIndex(read.getReferenceIndex());
setAlignmentStart(read.getAlignmentStart());
mReadNameLength = (short)read.getReadNameLength();
setMappingQuality(read.getMappingQuality());
mCigarLength = read.getCigarLength();
setFlags(read.getFlags());
mReadLength = read.getReadLength();
setMateReferenceIndex(read.getMateReferenceIndex());
setMateAlignmentStart(read.getMateAlignmentStart());
setInferredInsertSize(read.getInferredInsertSize());
mRestOfBinaryData = null;
super.setReadName(read.getReadName());
super.setCigarString(read.getCigarString());
super.setReadBases(read.getReadBases());
super.setBaseQualities(read.getBaseQualities());
SAMReadGroupRecord samRG = read.getReadGroup();
clearAttributes();
if (samRG != null) {
GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
setReadGroup(rg);
}
List<SAMTagAndValue> attributes = read.getAttributes();
for(SAMTagAndValue tagAndValue : attributes) {
setAttribute(tagAndValue.tag, tagAndValue.value);
}
}