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

GATKSAMRecord.getMateReferenceIndex介绍

暂无

代码示例

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

this.with_itself_and_mate_mapped++;
if (!read.getReferenceIndex().equals(read.getMateReferenceIndex())) {
  this.with_mate_mapped_to_a_different_chr++;

代码示例来源：origin: broadgsa/gatk

emptyRead.setMateReferenceIndex(read.getMateReferenceIndex());
emptyRead.setMateAlignmentStart(read.getMateAlignmentStart());
emptyRead.setInferredInsertSize(read.getInferredInsertSize());