4861 …uble known12, double known21, double known22, double center_ct_d, double freq11, double freq12, do…  in calc_lnlike()  argument
4863   freq11 += freq11_incr;  in calc_lnlike()
4867   lnlike = center_ct_d * log(freq11 * freq22 + freq12 * freq21);  in calc_lnlike()
4869     lnlike += known11 * log(freq11);  in calc_lnlike()
4898   double freq11;  in em_phase_hethet()  local
4920   freq11 = known11 * twice_tot_recip;  in em_phase_hethet()
4924   prod_1122 = freq11 * freq22;  in em_phase_hethet()
4929   freq1x = freq11 + freq12 + half_hethet_share;  in em_phase_hethet()
4931   freqx1 = freq11 + freq21 + half_hethet_share;  in em_phase_hethet()
4935 …(0.5 * (freq11 + freq22 - freq12 - freq21 - 3 * half_hethet_share), 0.5 * (prod_1122 + prod_1221 +…  in em_phase_hethet()
4961       const double nonzero_freq_xx = freq11 + freq22;  in em_phase_hethet()
4975 …best_lnlike = calc_lnlike(known11, known12, known21, known22, center_ct_d, freq11, freq12, freq21,…  in em_phase_hethet()
4979 …cur_lnlike = calc_lnlike(known11, known12, known21, known22, center_ct_d, freq11, freq12, freq21, …  in em_phase_hethet()
4987       if (freqx1 * freq1x >= freq11) {  in em_phase_hethet()
4988 	dxx = freq1x * freqx1 - freq11;  in em_phase_hethet()
4998       if ((freq11 + best_sol) - freqx1 * freq1x >= 0.0) {  in em_phase_hethet()
5031     freq11 += best_sol;  in em_phase_hethet()
5039   *freq11_ptr = freq11;  in em_phase_hethet()
5104   double freq11;  in ld_dprime_thread()  local
5196 	if (em_phase_hethet_nobase(counts, is_x1, is_x2, &freq1x, &freq2x, &freqx1, &freqx2, &freq11)) {  in ld_dprime_thread()
5204 	dxx = freq11 - freq11_expected; // D  in ld_dprime_thread()
7922   double freq11;  in twolocus()  local
8118     freq11 = (double)(2 * counts_all[0] + counts_all[2] + counts_all[8]);  in twolocus()
8124         freq11 -= (double)((int32_t)counts_cc[16]);  in twolocus()
8129         freq11 -= ((double)(2 * counts_cc[16] + counts_cc[18])) * (1.0 - SQRT_HALF);  in twolocus()
8134         freq11 -= ((double)(2 * counts_cc[16] + counts_cc[24])) * (1.0 - SQRT_HALF);  in twolocus()
8140     twice_tot_recip = 1.0 / (freq11 + freq12 + freq21 + freq22 + 2 * ((int32_t)counts_all[10]));  in twolocus()
8141     freq11 *= twice_tot_recip;  in twolocus()
8146     freq1x = freq11 + freq12 + half_hethet_share;  in twolocus()
8148     freqx1 = freq11 + freq21 + half_hethet_share;  in twolocus()
8154       if ((freq11 * freq22 != 0.0) || (freq12 * freq21 != 0.0)) {  in twolocus()
8159 …freq11 + freq22 - freq12 - freq21 - 3 * half_hethet_share), 0.5 * (freq11 * freq22 + freq12 * freq…  in twolocus()
8188         const double nonzero_freq_xx = freq11 + freq22;  in twolocus()
8224       dxx = freq11 + solutions[ulkk] - freqx1 * freq1x; // D  in twolocus()
8249       bufptr = dtoa_f_w9p6_spaced(freq11 + solutions[ulkk], bufptr);  in twolocus()
10457   double freq11;  in indep_pairphase()  local
10638 …    if (!em_phase_hethet_nobase(counts, is_x, is_x, &freq1x, &freq2x, &freqx1, &freqx2, &freq11)) {  in indep_pairphase()
10640 		rsq = freq11 - freq11_expected;  in indep_pairphase()
11376   double freq11;  in test_mishap()  local
11529 	    em_phase_hethet_nobase(&(counts[18]), 0, 0, &dxx, &dyy, &dzz, &dww, &freq11);  in test_mishap()
11533 …dxx = (freq11 * tot_recip - (hap_ct_table[2] + hap_ct_table[3])) / ((double)((int32_t)(counts[4] +…  in test_mishap()
12769   double freq11;  in clump_reports()  local
13416 …    if (!em_phase_hethet_nobase(counts, is_x, is_x, &freq1x, &freq2x, &freqx1, &freqx2, &freq11)) {  in clump_reports()
13418 	dxx = freq11 - freq11_expected;  in clump_reports()
13546 …    if (!em_phase_hethet_nobase(counts, is_x, is_x, &freq1x, &freq2x, &freqx1, &freqx2, &freq11)) {  in clump_reports()
13548 	dxx = freq11 - freq11_expected;  in clump_reports()