Imported Upstream version 0.1.18

[samtools.git] / bcftools / em.c

diff --git a/bcftools/em.c b/bcftools/em.c
index 32b400ff70f63ebf71e26bf94ce5bd9af8434859..b7dfe1a2889e08de37deb725dd7569d963bdab91 100644 (file)
--- a/bcftools/em.c
+++ b/bcftools/em.c
@@ -168,7 +168,6 @@ static double lk_ratio_test(int n, int n1, const double *pdg, double f3[3][3])
 // x[5..6]: group1 freq, group2 freq
 // x[7]: 1-degree P-value
 // x[8]: 2-degree P-value
-// x[9]: 1-degree P-value with freq estimated from genotypes
 int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10])
 {
        double *pdg;
@@ -208,11 +207,13 @@ int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10])
                x[6] = freqml(x[0], n1, n, pdg);
        }
        if ((flag & 1<<7) && n1 > 0 && n1 < n) { // 1-degree P-value
-               double f[3], f3[3][3];
+               double f[3], f3[3][3], tmp;
                f[0] = x[0]; f[1] = x[5]; f[2] = x[6];
                for (i = 0; i < 3; ++i)
                        f3[i][0] = (1-f[i])*(1-f[i]), f3[i][1] = 2*f[i]*(1-f[i]), f3[i][2] = f[i]*f[i];
-               x[7] = kf_gammaq(.5, log(lk_ratio_test(n, n1, pdg, f3)));
+               tmp = log(lk_ratio_test(n, n1, pdg, f3));
+               if (tmp < 0) tmp = 0;
+               x[7] = kf_gammaq(.5, tmp);
        }
        if ((flag & 3<<8) && n1 > 0 && n1 < n) { // 2-degree P-value
                double g[3][3], tmp;
@@ -222,8 +223,8 @@ int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10])
                for (i = 0; i < ITER_MAX; ++i)
                        if (g3_iter(g[2], pdg, n1, n) < EPS) break;
                tmp = log(lk_ratio_test(n, n1, pdg, g));
+               if (tmp < 0) tmp = 0;
                x[8] = kf_gammaq(1., tmp);
-               x[9] = kf_gammaq(.5, tmp);
        }
        // free
        free(pdg);