genReadFileNames(readFN, i, read_type, s, readFs);
ReadReader<SingleReadQ> reader(s, readFs, refs->hasPolyA(), seedLen); // allow calculation of calc_lq() function
genReadFileNames(readFN, i, read_type, s, readFs);
ReadReader<SingleReadQ> reader(s, readFs, refs->hasPolyA(), seedLen); // allow calculation of calc_lq() function