Merge commit 'upstream/0.1.13'

[samtools.git] / bcftools / ld.c

diff --git a/bcftools/ld.c b/bcftools/ld.c
index aa7ec072b2c7fc2e60ea3d1fe8145711a8841d28..11474ed422aa40e5b839831a5c0b5ab80f5c73ad 100644 (file)
--- 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;