//read bases
read->bases = new char(numBases);
in.read(read->bases, numBases);
tempBuf = buffer;
if (tempBuf.length() > numBases) { tempBuf = tempBuf.substr(0, numBases); strcpy(read->bases, tempBuf.c_str()); }
//read bases
read->bases = new char(numBases);
in.read(read->bases, numBases);
tempBuf = buffer;
if (tempBuf.length() > numBases) { tempBuf = tempBuf.substr(0, numBases); strcpy(read->bases, tempBuf.c_str()); }