minor changes

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 0cc2d6b6710dbedc53f89803971e8170233396eb..195a59602ab4e778084b6eefc105ee1d608643bb 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -531,8 +531,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                s.l = s.m = 0; s.s = 0;
                puts("##fileformat=VCFv4.0");
                puts("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">");
-//             puts("##INFO=<ID=AF,Number=1,Type=Float,Description=\"Posterior non-reference allele frequency\">");
-//             puts("##INFO=<ID=AFEM,Number=1,Type=Float,Description=\"Prior-free non-reference allele frequency by EM\">");
+               puts("##INFO=<ID=AF,Number=1,Type=Float,Description=\"Non-reference allele frequency \\argmax_f P(D|f)\">");
+               puts("##INFO=<ID=AFE,Number=1,Type=Float,Description=\"Expected non-reference allele frequency\">");
                puts("##FILTER=<ID=Q13,Description=\"All min{baseQ,mapQ} below 13\">");
                kputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", &s);
                for (i = 0; i < n; ++i) {
@@ -602,15 +602,16 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        printf("DP=%d;MQ=%d", depth, rms_q);
                        if (tot) {
                                printf(";AF=%.3lf", 1. - r.f_em);
+                               if (level >= 2) printf(";AFE=%.3lf", 1-r.f_exp);
                                if (conf->flag & MPLP_AFALL) {
-                                       printf(";AF0=%.3lf;AFN=%.3lf;AFE=%.3lf", 1-r.f_naive, 1-r.f_nielsen, 1-r.f_exp);
+                                       printf(";AF0=%.3lf;AFN=%.3lf", 1-r.f_naive, 1-r.f_nielsen);
                                        if (conf->flag & MPLP_AFS) printf(";AFB=%.3lf", 1-r.f_map);
                                }
                        }
                        printf("\tGT:GQ:DP");
                        if (tot) {
                                for (i = 0; i < n; ++i) {
-                                       int x = mc_call_gt(ma, r.f_em, i);
+                                       int x = mc_call_gt(ma, r.f_exp, i);
                                        printf("\t%c/%c:%d:%d", "10"[((x&3)==2)], "10"[((x&3)>0)], x>>2, n_plp[i]);
                                }
                        } else for (i = 0; i < n; ++i) printf("\t./.:0:0");