本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.getFlags()
方法的一些代码示例,展示了GATKSAMRecord.getFlags()
的具体用法。这些代码示例主要来源于Github
/Stackoverflow
/Maven
等平台,是从一些精选项目中提取出来的代码,具有较强的参考意义,能在一定程度帮忙到你。GATKSAMRecord.getFlags()
方法的具体详情如下:
包路径:org.broadinstitute.gatk.utils.sam.GATKSAMRecord
类名称:GATKSAMRecord
方法名:getFlags
暂无
代码示例来源:origin: broadgsa/gatk-protected
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (!(o instanceof GATKSAMRecordHashWrapper)) {
return false;
}
GATKSAMRecord other = ((GATKSAMRecordHashWrapper) o).samRec;
return samRec.getReadName().equals(other.getReadName()) && samRec.getFlags() == other.getFlags();
}
代码示例来源:origin: broadgsa/gatk-protected
public int hashCode() {
// Use a murmur hash of the flags to distribute the values more uniformly over the full range of int
return samRec.getReadName().hashCode() + (31 * murmurHasher.hashLong(samRec.getFlags()).asInt());
}
}
代码示例来源:origin: broadgsa/gatk-protected
/**
* Creates a hard-clipped view on a existing read record.
* @param read the underlying unclipped read.
* @param start inclusive first position in {@code read} included in the clipped view.
* @param end inclusive last position in {@code read} included in the clipped view.
*/
public ClippedGATKSAMRecord(final GATKSAMRecord read, int start, int end) {
super(read.getHeader());
this.setReferenceIndex(read.getReferenceIndex());
this.setAlignmentStart(read.getAlignmentStart() + start);
this.setMappingQuality(100);
// setting read indexing bin below
this.setFlags(read.getFlags());
this.setMateReferenceIndex(read.getMateReferenceIndex());
this.setMateAlignmentStart(read.getMateAlignmentStart());
this.setInferredInsertSize(read.getInferredInsertSize());
this.setReadBases(Arrays.copyOfRange(read.getReadBases(), start, end));
this.setBaseQualities(Arrays.copyOfRange(read.getBaseQualities(),start,end));
this.setReadName(read.getReadName());
insertionQuals = Arrays.copyOfRange(read.getBaseInsertionQualities(),start,end);
deletionQuals = Arrays.copyOfRange(read.getBaseDeletionQualities(),start,end);
// Set these to null in order to mark them as being candidates for lazy initialization.
// If this is not done, they will have non-null defaults.
super.setReadName(null);
super.setCigarString(null);
super.setReadBases(null);
super.setBaseQualities(null);
// Do this after the above because setCigarString will clear it.
GATKBin.setReadIndexingBin(this, -1);
}
代码示例来源:origin: broadgsa/gatk
emptyRead.setMappingQuality(0);
emptyRead.setFlags(read.getFlags());
emptyRead.setMateReferenceIndex(read.getMateReferenceIndex());
emptyRead.setMateAlignmentStart(read.getMateAlignmentStart());
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