void SamFormatParser::ParseRGLine(const string& line) {
SamReadGroup rg;
// split string into tokens
vector<string> tokens = Split(line, Constants::SAM_TAB);
// iterate over tokens
vector<string>::const_iterator tokenIter = tokens.begin();
vector<string>::const_iterator tokenEnd = tokens.end();
for ( ; tokenIter != tokenEnd; ++tokenIter ) {
// get token tag/value
const string tokenTag = (*tokenIter).substr(0,2);
const string tokenValue = (*tokenIter).substr(3);
// set read group contents
if ( tokenTag == Constants::SAM_RG_ID_TAG ) rg.ID = tokenValue;
else if ( tokenTag == Constants::SAM_RG_SAMPLE_TAG ) rg.Sample = tokenValue;
else if ( tokenTag == Constants::SAM_RG_LIBRARY_TAG ) rg.Library = tokenValue;
else if ( tokenTag == Constants::SAM_RG_DESCRIPTION_TAG ) rg.Description = tokenValue;
else if ( tokenTag == Constants::SAM_RG_PLATFORMUNIT_TAG ) rg.PlatformUnit = tokenValue;
else if ( tokenTag == Constants::SAM_RG_PREDICTEDINSERTSIZE_TAG ) rg.PredictedInsertSize = tokenValue;
else if ( tokenTag == Constants::SAM_RG_SEQCENTER_TAG ) rg.SequencingCenter = tokenValue;
else if ( tokenTag == Constants::SAM_RG_PRODUCTIONDATE_TAG ) rg.ProductionDate = tokenValue;
else if ( tokenTag == Constants::SAM_RG_SEQTECHNOLOGY_TAG ) rg.SequencingTechnology = tokenValue;
else
cerr << "SamFormatParser ERROR: unknown RG tag: " << tokenTag << endl;
}
// if @RG line exists, ID must be provided
if ( !rg.HasID() ) {
cerr << "SamFormatParser ERROR: @RG line is missing ID tag" << endl;
return;
}
// if @RG line exists, SM must be provided
if ( !rg.HasSample() ) {
cerr << "SamFormatParser ERROR: @RG line is missing SM tag" << endl;
return;
}
// store SAM read group entry
m_header.ReadGroups.Add(rg);
}
void SamFormatParser::ParseRGLine(const string& line) {
SamReadGroup rg;
// split string into tokens
vector<string> tokens = Split(line, Constants::SAM_TAB);
// iterate over tokens
vector<string>::const_iterator tokenIter = tokens.begin();
vector<string>::const_iterator tokenEnd = tokens.end();
for ( ; tokenIter != tokenEnd; ++tokenIter ) {
// get token tag/value
const string tokenTag = (*tokenIter).substr(0,2);
const string tokenValue = (*tokenIter).substr(3);
// set read group contents
if ( tokenTag == Constants::SAM_RG_ID_TAG ) rg.ID = tokenValue;
else if ( tokenTag == Constants::SAM_RG_DESCRIPTION_TAG ) rg.Description = tokenValue;
else if ( tokenTag == Constants::SAM_RG_FLOWORDER_TAG ) rg.FlowOrder = tokenValue;
else if ( tokenTag == Constants::SAM_RG_KEYSEQUENCE_TAG ) rg.KeySequence = tokenValue;
else if ( tokenTag == Constants::SAM_RG_LIBRARY_TAG ) rg.Library = tokenValue;
else if ( tokenTag == Constants::SAM_RG_PLATFORMUNIT_TAG ) rg.PlatformUnit = tokenValue;
else if ( tokenTag == Constants::SAM_RG_PREDICTEDINSERTSIZE_TAG ) rg.PredictedInsertSize = tokenValue;
else if ( tokenTag == Constants::SAM_RG_PRODUCTIONDATE_TAG ) rg.ProductionDate = tokenValue;
else if ( tokenTag == Constants::SAM_RG_PROGRAM_TAG ) rg.Program = tokenValue;
else if ( tokenTag == Constants::SAM_RG_SAMPLE_TAG ) rg.Sample = tokenValue;
else if ( tokenTag == Constants::SAM_RG_SEQCENTER_TAG ) rg.SequencingCenter = tokenValue;
else if ( tokenTag == Constants::SAM_RG_SEQTECHNOLOGY_TAG ) rg.SequencingTechnology = tokenValue;
else { // custom tag
CustomHeaderTag otherTag;
otherTag.TagName = tokenTag;
otherTag.TagValue = tokenValue;
rg.CustomTags.push_back(otherTag);
}
}
// check for required tags
if ( !rg.HasID() )
throw BamException("SamFormatParser::ParseRGLine", "@RG line is missing ID tag");
// store SAM read group entry
m_header.ReadGroups.Add(rg);
}
