* samtools-0.1.8-6 (r638)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 195a59602ab4e778084b6eefc105ee1d608643bb..a1c87ab6f67831fe4f949a4625f5cd685b72317d 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -584,8 +584,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        ++N; // number of processed lines
                        printf("%s\t%d\t.\t%c\t", h->target_name[tid], pos + 1, _ref0b);
                        if (is_var) {
-                               if (_ref0 == r.ref) putchar("ACGTN"[r.alt]);
-                               else printf("%c,%c", "ACGTN"[r.ref], "ACGTN"[r.alt]);
+                               putchar("ACGTN"[r.alt]);
+                               if (r.alt2 >= 0 && r.alt2 < 4) printf(",%c", "ACGT"[r.alt2]);
                        } else putchar('.');
                        printf("\t%d\t", qref);
                        if (!tot) printf("Q13\t");
@@ -665,10 +665,18 @@ int bam_mpileup(int argc, char *argv[])
        mplp.max_mq = 60;
        mplp.prior_type = MC_PTYPE_FULL;
        mplp.theta = 1e-3;
-       while ((c = getopt(argc, argv, "vVcF2Sf:r:l:VM:q:t:")) >= 0) {
+       while ((c = getopt(argc, argv, "vVcFSP:f:r:l:VM:q:t:")) >= 0) {
                switch (c) {
                case 't': mplp.theta = atof(optarg); break;
-               case '2': mplp.prior_type = MC_PTYPE_COND2; break;
+               case 'P':
+                       if (strcmp(optarg, "full") == 0) mplp.prior_type = MC_PTYPE_FULL;
+                       else if (strcmp(optarg, "cond2") == 0) mplp.prior_type = MC_PTYPE_COND2;
+                       else if (strcmp(optarg, "flat") == 0) mplp.prior_type = MC_PTYPE_FLAT;
+                       else {
+                               fprintf(stderr, "[%s] unrecognized prior type.\n", __func__);
+                               return 1;
+                       }
+                       break;
                case 'f':
                        mplp.fai = fai_load(optarg);
                        if (mplp.fai == 0) return 1;
@@ -693,10 +701,10 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "         -M INT      cap mapping quality at INT [%d]\n", mplp.max_mq);
                fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
                fprintf(stderr, "         -t FLOAT    scaled mutation rate [%lg]\n", mplp.theta);
+               fprintf(stderr, "         -P STR      prior: full, flat, cond2 [full]");
                fprintf(stderr, "         -c          generate VCF output (consensus calling)\n");
                fprintf(stderr, "         -v          show variant sites only\n");
                fprintf(stderr, "         -S          calculate AFS (slow, to stderr)\n");
-               fprintf(stderr, "         -2          conditional prior\n");
                fprintf(stderr, "\n");
                fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n");
                return 1;