本文整理汇总了Java中htsjdk.samtools.SAMRecord.getFirstOfPairFlag方法的典型用法代码示例。如果您正苦于以下问题：Java SAMRecord.getFirstOfPairFlag方法的具体用法？Java SAMRecord.getFirstOfPairFlag怎么用？Java SAMRecord.getFirstOfPairFlag使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类htsjdk.samtools.SAMRecord的用法示例。
在下文中一共展示了SAMRecord.getFirstOfPairFlag方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: processRecord
import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
public int processRecord(SAMRecord sr, Object2IntOpenHashMap<String> readLoadingSet){
int totalOp = 0;
String hlagene = HLA.extractHLAGeneName(sr.getReferenceName());
HLAGraph hg = this.hlaName2Graph.get(hlagene);
//hg.traverse();
if(hg != null){
if(hg.isClassI()){
boolean qc = this.qcCheck(sr);
if(!qc)
return 0;
}
int readnum = readLoadingSet.getInt(sr.getReadName());
//no such read has been read. return value of 0 means the hashSet doesn't have the read
if(readnum == 0){
readnum = sr.getFirstOfPairFlag() ? HLA.readNum : 0-HLA.readNum;
readLoadingSet.put(sr.getReadName(), HLA.readNum);
HLA.readNum++;
}else
readnum = sr.getFirstOfPairFlag() ? readnum : 0-readnum;
totalOp += hg.addWeight(sr, readnum);//HLA.readNum);
//HLA.readNum++;
}else{
;//HLA.log.appendln("UNKNOWN HLA GENE: " + hlagene);
}
return totalOp;
}