bool BamRecord::initFromFile(BamFileReader *bamFileReader)
{
setFileIdx(bamFileReader->getFileIdx());
_bamAlignment = bamFileReader->getAlignment();
bamFileReader->getChrName(_chrName);
_bamChromId = bamFileReader->getCurrChromdId();
_startPos = bamFileReader->getStartPos();
int2str(_startPos, _startPosStr);
_endPos = bamFileReader->getEndPos();
int2str(_endPos, _endPosStr);
bamFileReader->getName(_name);
bamFileReader->getScore(_score);
char strandChar = bamFileReader->getStrand();
setStrand(strandChar);
_isUnmapped = !bamFileReader->getAlignment().IsMapped();
_isMateUnmapped = !bamFileReader->getAlignment().IsMateMapped();
// Get the cigar data into a string.
buildCigarStr();
bamFileReader->getMateChrName(_mateChrName);
int2str(_bamAlignment.MatePosition, _matePos);
int2str(_bamAlignment.InsertSize, _insertSize);
_queryBases = _bamAlignment.QueryBases;
_qualities = _bamAlignment.Qualities;
return true;
}
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 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 Bed3Interval::initFromFile(SingleLineDelimTextFileReader *fileReader)
{
setFileIdx(fileReader->getFileIdx());
fileReader->getField(0, _chrName);
fileReader->getField(1, _startPosStr);
fileReader->getField(2, _endPosStr);
_startPos = str2chrPos(_startPosStr);
_endPos = str2chrPos(_endPosStr);
return true;
}
