X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fld.c;h=11474ed422aa40e5b839831a5c0b5ab80f5c73ad;hp=dc84d4b02d836f0a07a0736588dd1142485d10cf;hb=c34624801b980425af68c3c431423c72b18c14fe;hpb=f2f3968e11eead9ce5601b01890bc2339ff951e9

diff --git a/bcftools/ld.c b/bcftools/ld.c
index dc84d4b..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