本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.getUnclippedStart()方法的一些代码示例，展示了GATKSAMRecord.getUnclippedStart()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.getUnclippedStart()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：getUnclippedStart

GATKSAMRecord.getUnclippedStart介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

/**
 * Determines the original alignment start 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 start of a read before it was clipped
 */
public int getOriginalAlignmentStart() {
  return getUnclippedStart();
}

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 uStart = read.getUnclippedStart();
int uStop = read.getUnclippedEnd();