本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.getUnclippedEnd()
方法的一些代码示例,展示了GATKSAMRecord.getUnclippedEnd()
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.getUnclippedEnd()
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:getUnclippedEnd
暂无
代码示例来源:origin: broadgsa/gatk
/**
* Determines the original alignment end of a previously clipped read.
*
* This is useful for reads that have been trimmed to a variant region and lost the information of it's original alignment end
*
* @return the alignment end of a read before it was clipped
*/
public int getOriginalAlignmentEnd() {
return getUnclippedEnd();
}
代码示例来源:origin: broadgsa/gatk
private static boolean unclippedReadOverlapsRegion(final GATKSAMRecord sampleRead, final int referenceIndex, final int start, final int end) {
final int readReference = sampleRead.getReferenceIndex();
if (readReference != referenceIndex)
return false;
final int readStart = sampleRead.getUnclippedStart();
if (readStart > end)
return false;
final int readEnd = sampleRead.getReadUnmappedFlag() ? sampleRead.getUnclippedEnd()
: Math.max(sampleRead.getUnclippedEnd(), sampleRead.getUnclippedStart());
return readEnd >= start;
}
代码示例来源:origin: broadgsa/gatk
/**
* Asserts that clipping doesn't change the getUnclippedStart / getUnclippedEnd
*
* @param original original read
* @param clipped clipped read
*/
private void assertUnclippedLimits(GATKSAMRecord original, GATKSAMRecord clipped) {
if (CigarUtils.readHasNonClippedBases(clipped)) {
Assert.assertEquals(original.getUnclippedStart(), clipped.getUnclippedStart());
Assert.assertEquals(original.getUnclippedEnd(), clipped.getUnclippedEnd());
}
}
代码示例来源:origin: broadgsa/gatk-protected
read.getUnclippedStart(), read.getAlignmentEnd(), read.getUnclippedEnd(),
read.getCigarString(), readLikelihoods[i][j]);
代码示例来源:origin: broadgsa/gatk
int sStop = read.getSoftEnd();
int uStart = read.getUnclippedStart();
int uStop = read.getUnclippedEnd();
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