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

GATKSAMRecord.getProperPairFlag介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk-protected

/**
 * Account for the read and check it for any statistics necessary. Reads are marked in the temporary
 * attribute "seen" to make sure they're not counted twice.
 * 
 * @param read the read
 */
private void processRead(GATKSAMRecord read) {
  if (read.getTemporaryAttribute("seen") == null) {
    nReads++;
    if (read.getReadPairedFlag() && !read.getProperPairFlag())
      nBadMates++;
    read.setTemporaryAttribute("seen", true);
  }
}

代码示例来源：origin: broadgsa/gatk

this.read1++;
if (read.getProperPairFlag()) {
  this.properly_paired++;

代码示例来源：origin: broadgsa/gatk

rawDepth++;
if (base.getRead().getReadPairedFlag() && (base.getRead().getMateUnmappedFlag() || !base.getRead().getProperPairFlag())){
  improperPairsCount++;
  continue;