本文整理汇总了C++中SamRecord::setReadName方法的典型用法代码示例。如果您正苦于以下问题：C++ SamRecord::setReadName方法的具体用法？C++ SamRecord::setReadName怎么用？C++ SamRecord::setReadName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SamRecord的用法示例。
在下文中一共展示了SamRecord::setReadName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C++代码示例。
示例1: main
//.........这里部分代码省略.........
else if ( static_cast<int>(fastaFile.vnSequenceLengths[i]) != atoi(pSamHeaderRecord->getTagValue("LN")) ) {
gpLogger->error("SequenceLength is not identical between fasta and input BAM file");
}
else {
if ( !sAS.empty() )
samHeader.setSQTag("AS",sAS.c_str(),fastaFile.vsSequenceNames[i].c_str());
samHeader.setSQTag("M5",fastaFile.vsMD5sums[i].c_str(),fastaFile.vsSequenceNames[i].c_str());
if ( !sUR.empty() )
samHeader.setSQTag("UR",sUR.c_str(),fastaFile.vsSequenceNames[i].c_str());
if ( !sSP.empty() )
samHeader.setSQTag("SP",sSP.c_str(),fastaFile.vsSequenceNames[i].c_str());
}
}
gpLogger->write_log("Finished checking the consistency of SQ tags");
}
else {
gpLogger->write_log("Skipped checking the consistency of SQ tags");
}
// go over the headers again,
// assuming order of HD, SQ, RG, PG, and put proper tags at the end of the original tags
gpLogger->write_log("Creating the header of new output file");
//SamFileHeader outHeader;
samHeader.resetHeaderRecordIter();
for(unsigned int i=0; i < vsHDHeaders.size(); ++i) {
samHeader.addHeaderLine(vsHDHeaders[i].c_str());
}
/*
for(int i=0; i < fastaFile.vsSequenceNames.size(); ++i) {
std::string s("@SQ\tSN:");
char buf[1024];
s += fastaFile.vsSequenceNames[i];
sprintf(buf,"\tLN:%d",fastaFile.vnSequenceLengths[i]);
s += buf;
if ( !sAS.empty() ) {
sprintf(buf,"\tAS:%s",sAS.c_str());
s += buf;
}
if ( !sUR.empty() ) {
sprintf(buf,"\tUR:%s",sUR.c_str());
s += buf;
}
sprintf(buf,"\tM5:%s",fastaFile.vsMD5sums[i].c_str());
s += buf;
if ( !sSP.empty() ) {
sprintf(buf,"\tSP:%s",sSP.c_str());
s += buf;
}
outHeader.addHeaderLine(s.c_str());
}*/
for(unsigned int i=0; i < vsRGHeaders.size(); ++i) {
samHeader.addHeaderLine(vsRGHeaders[i].c_str());
}
for(unsigned int i=0; i < vsPGHeaders.size(); ++i) {
samHeader.addHeaderLine(vsPGHeaders[i].c_str());
}
samOut.WriteHeader(samHeader);
gpLogger->write_log("Adding %d HD, %d RG, and %d PG headers",vsHDHeaders.size(), vsRGHeaders.size(), vsPGHeaders.size());
gpLogger->write_log("Finished writing output headers");
// parse RG tag and get RG ID to append
std::string sRGID;
if ( ! vsRGHeaders.empty() ) {
std::vector<std::string> tokens;
FastaFile::tokenizeString( vsRGHeaders[0].c_str(), tokens );
for(unsigned int i=0; i < tokens.size(); ++i) {
if ( tokens[i].find("ID:") == 0 ) {
sRGID = tokens[i].substr(3);
}
}
}
gpLogger->write_log("Writing output BAM file");
SamRecord samRecord;
while (samIn.ReadRecord(samHeader, samRecord) == true) {
if ( !sRGID.empty() ) {
if ( samRecord.addTag("RG",'Z',sRGID.c_str()) == false ) {
gpLogger->error("Failed to add a RG tag %s",sRGID.c_str());
}
// temporary code added
if ( strncmp(samRecord.getReadName(),"seqcore_",8) == 0 ) {
char buf[1024];
sprintf(buf,"UM%s",samRecord.getReadName()+8);
samRecord.setReadName(buf);
}
}
samOut.WriteRecord(samHeader, samRecord);
//if ( samIn.GetCurrentRecordCount() == 1000 ) break;
}
samOut.Close();
gpLogger->write_log("Successfully written %d records",samIn.GetCurrentRecordCount());
delete gpLogger;
return 0;
}