本文整理汇总了C++中SamFileHeader::appendCommentLines方法的典型用法代码示例。如果您正苦于以下问题：C++ SamFileHeader::appendCommentLines方法的具体用法？C++ SamFileHeader::appendCommentLines怎么用？C++ SamFileHeader::appendCommentLines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::appendCommentLines方法的2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: parseOutRG
void parseOutRG(SamFileHeader& header, std::string& noRgPgString, SamFileHeader* newHeader)
{
noRgPgString.clear();
// strings for comparing if two RGs with same ID are the same.
static std::string prevString = "";
static std::string newString = "";
SamHeaderRecord* rec = header.getNextHeaderRecord();
while(rec != NULL)
{
if(rec->getType() == SamHeaderRecord::RG)
{
if(newHeader != NULL)
{
// This is an RG line.
// First check if this RG is already included in the new header.
SamHeaderRG* prevRG = newHeader->getRG(rec->getTagValue("ID"));
if(prevRG != NULL)
{
// This RG already exists, check that they are the same.
// If they are the same, there is nothing to do.
bool status = true;
prevString.clear();
newString.clear();
status &= prevRG->appendString(prevString);
status &= rec->appendString(newString);
if(prevString != newString)
{
// They are not identical, so report an error.
Logger::gLogger->error("Failed to add readgroup to header, "
"duplicate, but non-identical RG ID, %s",
rec->getTagValue("ID"));
}
}
else
{
// This RG does not exist yet, so add it to the new header.
if(!newHeader->addRecordCopy((SamHeaderRG&)(*rec)))
{
// Failed to add the RG, exit.
Logger::gLogger->error("Failed to add readgroup to header, %s",
newHeader->getErrorMessage());
}
}
}
}
else if(rec->getType() == SamHeaderRecord::PG)
{
if(newHeader != NULL)
{
// This is a PG line.
// First check if this PG is already included in the new header.
SamHeaderPG* prevPG = newHeader->getPG(rec->getTagValue("ID"));
if(prevPG != NULL)
{
// This PG already exists, check if they are the same.
// If they are the same, there is nothing to do.
bool status = true;
prevString.clear();
newString.clear();
status &= prevPG->appendString(prevString);
status &= rec->appendString(newString);
if(prevString != newString)
{
// They are not identical, ignore for now.
// TODO: change the ID, and add it.
Logger::gLogger->warning("Warning: dropping duplicate, "
"but non-identical PG ID, %s",
rec->getTagValue("ID"));
}
}
else
{
// This PG does not exist yet, so add it to the new header.
if(!newHeader->addRecordCopy((SamHeaderPG&)(*rec)))
{
// Failed to add the PG, exit.
Logger::gLogger->error("Failed to add PG to header, %s",
newHeader->getErrorMessage());
}
}
}
}
else
{
rec->appendString(noRgPgString);
}
rec = header.getNextHeaderRecord();
}
// Append the comments.
header.appendCommentLines(noRgPgString);
}示例2: parseOutRG
//.........这里部分代码省略.........
prevPIEnd = newPIStart;
}
else
{
prevPIEnd = prevString.find('\t', prevPIStart) + 1;
}
if(newPIStart == std::string::npos)
{
// new string has PI, so compare to the start of that.
newPIStart = prevPIStart;
newPIEnd = newPIStart;
}
else
{
newPIEnd = newString.find('\t', newPIStart) + 1;
}
// Compare before PI.
if((newString.compare(0, newPIStart, prevString, 0, prevPIStart) != 0) ||
(newString.compare(newPIEnd, std::string::npos, prevString,
prevPIEnd, std::string::npos) != 0))
{
// They are not identical, so report an error.
Logger::gLogger->error("Failed to add readgroup to header, "
"duplicate, but non-identical RG ID, %s, "
"even when ignoring PI\n"
"prev:\t(%s)\nnew:\t(%s)",
rec->getTagValue("ID"),
prevString.c_str(),
newString.c_str());
}
else
{
Logger::gLogger->warning("Warning: ignoring non-identical PI field "
"for RG ID, %s",
rec->getTagValue("ID"));
}
}
}
}
}
else
{
// This RG does not exist yet, so add it to the new header.
if(!newHeader->addRecordCopy((SamHeaderRG&)(*rec)))
{
// Failed to add the RG, exit.
Logger::gLogger->error("Failed to add readgroup to header, %s",
newHeader->getErrorMessage());
}
}
}
}
else if(rec->getType() == SamHeaderRecord::PG)
{
if(newHeader != NULL)
{
// This is a PG line.
// First check if this PG is already included in the new header.
SamHeaderPG* prevPG = newHeader->getPG(rec->getTagValue("ID"));
if(prevPG != NULL)
{
// This PG already exists, check if they are the same.
// If they are the same, there is nothing to do.
bool status = true;
prevString.clear();
newString.clear();
status &= prevPG->appendString(prevString);
status &= rec->appendString(newString);
if(prevString != newString)
{
// They are not identical, ignore for now.
// TODO: change the ID, and add it.
Logger::gLogger->warning("Warning: dropping duplicate, "
"but non-identical PG ID, %s",
rec->getTagValue("ID"));
}
}
else
{
// This PG does not exist yet, so add it to the new header.
if(!newHeader->addRecordCopy((SamHeaderPG&)(*rec)))
{
// Failed to add the PG, exit.
Logger::gLogger->error("Failed to add PG to header, %s",
newHeader->getErrorMessage());
}
}
}
}
else
{
rec->appendString(noRgPgString);
}
rec = header.getNextHeaderRecord();
}
// Append the comments.
header.appendCommentLines(noRgPgString);
}