bool checkAlignmentTag(const PropertyFilterValue& valueFilter, const BamAlignment& al) {
// ensure filter contains string data
Variant entireTagFilter = valueFilter.Value;
if ( !entireTagFilter.is_type<string>() ) return false;
// localize string from variant
const string& entireTagFilterString = entireTagFilter.get<string>();
// ensure we have at least "XX:x"
if ( entireTagFilterString.length() < 4 ) return false;
// get tagName & lookup in alignment
// if found, set tagType to tag type character
// if not found, return false
const string& tagName = entireTagFilterString.substr(0,2);
char tagType = '\0';
if ( !al.GetTagType(tagName, tagType) ) return false;
// remove tagName & ":" from beginning tagFilter
string tagFilterString = entireTagFilterString.substr(3);
// switch on tag type to set tag query value & parse filter token
int32_t intFilterValue, intQueryValue;
uint32_t uintFilterValue, uintQueryValue;
float realFilterValue, realQueryValue;
string stringFilterValue, stringQueryValue;
PropertyFilterValue tagFilter;
PropertyFilterValue::ValueCompareType compareType;
bool keepAlignment = false;
switch (tagType) {
// signed int tag type
case 'c' :
case 's' :
case 'i' :
if ( al.GetTag(tagName, intQueryValue) ) {
if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, intFilterValue, compareType) ) {
tagFilter.Value = intFilterValue;
tagFilter.Type = compareType;
keepAlignment = tagFilter.check(intQueryValue);
}
}
break;
// unsigned int tag type
case 'C' :
case 'S' :
case 'I' :
if ( al.GetTag(tagName, uintQueryValue) ) {
if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, uintFilterValue, compareType) ) {
tagFilter.Value = uintFilterValue;
tagFilter.Type = compareType;
keepAlignment = tagFilter.check(uintQueryValue);
}
}
break;
// 'real' tag type
case 'f' :
if ( al.GetTag(tagName, realQueryValue) ) {
if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, realFilterValue, compareType) ) {
tagFilter.Value = realFilterValue;
tagFilter.Type = compareType;
keepAlignment = tagFilter.check(realQueryValue);
}
}
break;
// string tag type
case 'A':
case 'Z':
case 'H':
if ( al.GetTag(tagName, stringQueryValue) ) {
if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, stringFilterValue, compareType) ) {
tagFilter.Value = stringFilterValue;
tagFilter.Type = compareType;
keepAlignment = tagFilter.check(stringQueryValue);
}
}
break;
// unknown tag type
default :
keepAlignment = false;
}
return keepAlignment;
}
