113     int32   aend      = _readData[_aID].rawLength - a3;  in trimRead()
118     int32   bend      = _readData[_bID].rawLength - b3;  in trimRead()
202     aend = std::min(amid + extension / 2, _readData[_aID].rawLength);  in trimRead()
205     bend = std::min(bmid + extension / 2 + bextra, _readData[_bID].rawLength);  in trimRead()
215     if (testAlignment(_aRead, abgn, aend, _readData[_aID].rawLength, _aID,  in trimRead()
216                       _bRead, bbgn, bend, _readData[_bID].rawLength, _bID,  in trimRead()
255       int32   ae = std::min(abgn + anchor,    _readData[_aID].rawLength);  in trimRead()
264           (be > _readData[_bID].rawLength)) {  in trimRead()
277       int32  ext = extend5(_aRead, ab, ae, _readData[_aID].rawLength, _aID,  in trimRead()
278                            _bRead, bb, be, _readData[_bID].rawLength, _bID,  in trimRead()
307       assert(ab <= _readData[_aID].rawLength);  in trimRead()
308       assert(bb <= _readData[_bID].rawLength);  in trimRead()
320            (aend < _readData[_aID].rawLength) &&  in trimRead()
321            (bend < _readData[_bID].rawLength)) {  in trimRead()
323       int32   ae = std::min(aend + extension, _readData[_aID].rawLength);  in trimRead()
329           (be > _readData[_bID].rawLength)) {  in trimRead()
338       int32  ext = extend3(_aRead, ab, ae, _readData[_aID].rawLength, _aID,  in trimRead()
339                            _bRead, bb, be, _readData[_bID].rawLength, _bID,  in trimRead()
368       assert(ae <= _readData[_aID].rawLength);  in trimRead()
369       assert(be <= _readData[_bID].rawLength);  in trimRead()
413               100.0 * (end - bgn) / _readData[_aID].rawLength);  in trimRead()
423             100.0 * (_readData[_aID].clrEnd - _readData[_aID].clrBgn) / _readData[_aID].rawLength);  in trimRead()