X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fld.c;h=11474ed422aa40e5b839831a5c0b5ab80f5c73ad;hp=aa7ec072b2c7fc2e60ea3d1fe8145711a8841d28;hb=1539c893f863596db71ab2af75a802e935496940;hpb=8d2494d1fb7cd0fa7c63be5ffba8dd1a11457522

diff --git a/bcftools/ld.c b/bcftools/ld.c
index aa7ec07..11474ed 100644
--- a/bcftools/ld.c
+++ b/bcftools/ld.c
@@ -70,7 +70,7 @@ double bcf_ld_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4])
 		for (i = 0; i < n_smpl; ++i) {
 			const uint8_t *pi = PL[j] + i * PL_len[j];
 			double *p = pdg[j] + i * 3;
-			p[0] = g_q2p[pi[b[j]->n_alleles]]; p[1] = g_q2p[pi[1]]; p[2] = g_q2p[pi[0]];
+			p[0] = g_q2p[pi[2]]; p[1] = g_q2p[pi[1]]; p[2] = g_q2p[pi[0]];
 		}
 	}
 	// iteration
@@ -80,7 +80,7 @@ double bcf_ld_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4])
 		memcpy(flast, f, 4 * sizeof(double));
 		freq_iter(n_smpl, pdg, f);
 		for (i = 0; i < 4; ++i) {
-			double x = fabs(f[0] - flast[0]);
+			double x = fabs(f[i] - flast[i]);
 			if (x > eps) eps = x;
 		}
 		if (eps < LD_ITER_EPS) break;