bool VcfRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
{
setFileIdx(fileReader->getFileIdx());
fileReader->getField(0, _chrName);
_chrId = fileReader->getCurrChromdId();
fileReader->getField(1, _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, _varAlt);
fileReader->getField(3, _varRef);
if (_varAlt[0] == '<') {
//this is a structural variant. Need to parse the tags to find the endpos.
_endPos = _startPos + fileReader->getVcfSVlen();
} else {
//endPos is just the startPos plus the length of the variant
_endPos = _startPos + _varRef.size();
}
int2str(_endPos, _endPosStr);
fileReader->getField(2, _name);
fileReader->getField(5, _score);
return initOtherFieldsFromFile(fileReader);
}
bool BedPlusInterval::initFromFile(SingleLineDelimTextFileReader *fileReader)
{
return (Bed6Interval::initFromFile(fileReader) && initOtherFieldsFromFile(fileReader));
}
