本文整理汇总了C++中SamFileHeader::resetHeaderRecordIter方法的典型用法代码示例。如果您正苦于以下问题：C++ SamFileHeader::resetHeaderRecordIter方法的具体用法？C++ SamFileHeader::resetHeaderRecordIter怎么用？C++ SamFileHeader::resetHeaderRecordIter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SamFileHeader的用法示例。
在下文中一共展示了SamFileHeader::resetHeaderRecordIter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.........
gpLogger->error("# of @SQ tags are different from the original BAM and the reference file");
}
// iterator over all @SQ objects
for(unsigned int i=0; i < numSQ; ++i) {
pSamHeaderRecord = samHeader.getSQ(fastaFile.vsSequenceNames[i].c_str());
if ( fastaFile.vsSequenceNames[i].compare(pSamHeaderRecord->getTagValue("SN")) != 0 ) {
gpLogger->error("SequenceName is not identical between fasta and input BAM file");
}
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());
}