fixed a typo

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index aa3e591a3d859f2ee834dcff6715d56920d99ca0..5a5c1cd1aba3e1c7e15a00638ee468186d052a52 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -161,7 +161,8 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
        kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
        kputs(b->info, &s);
        if (b->info[0]) kputc(';', &s);
-       ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
+//     ksprintf(&s, "AF1=%.4lg;AFE=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, 1.-pr->f_exp, pr->cil, pr->cih);
+       ksprintf(&s, "AF1=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, pr->cil, pr->cih);
        ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
        if (a.is_tested) {
                if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%lg,%lg,%lg,%lg", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]);
@@ -330,9 +331,9 @@ int bcfview(int argc, char *argv[])
                        bcf_2qcall(h, b);
                        continue;
                }
+               if (vc.flag & (VC_CALL|VC_ADJLD)) bcf_gl2pl(b);
                if (vc.flag & VC_CALL) { // call variants
                        bcf_p1rst_t pr;
-                       bcf_gl2pl(b);
                        bcf_p1_cal(b, p1, &pr); // pr.g[3] is not calculated here
                        if (vc.flag&VC_HWE) bcf_p1_cal_g3(p1, pr.g);
                        if (n_processed % 100000 == 0) {
@@ -348,7 +349,7 @@ int bcfview(int argc, char *argv[])
                                kstring_t s;
                                s.m = s.l = 0; s.s = 0;
                                if (*b->info) kputc(';', &s);
-                               ksprintf(&s, "NEIR=%.3lf", r2);
+                               ksprintf(&s, "NEIR=%.3lf;NEIF=%.3lf,%.3lf", r2, f[0]+f[2], f[0]+f[1]);
                                bcf_append_info(b, s.s, s.l);
                                free(s.s);
                        }