bool GffRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
{
setFileIdx(fileReader->getFileIdx());
fileReader->getField(0, _chrName);
fileReader->getField(3, _startPosStr);
_startPos = str2chrPos(_startPosStr);
_startPos--; // VCF is one-based. Here we intentionally don't decrement the string version,
//because we'll still want to output the one-based number in the print methods, even though
//internally we decrement the integer to comply with the 0-based format common to other records.
fileReader->getField(4, _endPosStr);
//endPos is just the startPos plus the length of the variant
_endPos = str2chrPos(_endPosStr);
fileReader->getField(2, _name);
fileReader->getField(1, _source);
fileReader->getField(5, _score);
//GFF allows a '.' for the strandChar, signifying it is not known.
fileReader->getField(6, _strand);
adjustStrandVal();
fileReader->getField(7, _frame);
_numFields = fileReader->getNumFields();
if (_numFields == 9) {
fileReader->getField(8, _group);
}
return true;
}
bool BedPlusInterval::initFromFile(SingleLineDelimTextFileReader *fileReader)
{
bool baseRetFlag = Bed3Interval::initFromFile(fileReader);
if (_numFixedFields != defaultNumFixedFields) {
fileReader->getField(3, _name);
fileReader->getField(4, _score);
fileReader->getField(5, _strand);
adjustStrandVal();
}
_plusFields.initFromFile(fileReader);
return baseRetFlag;
}
