* samtools-0.1.4-10 (r341)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 96f5c459df9dd88aa35d69a361898739016875d8..46f078a99e715a89ccc4f73119192fe8d1ef280c 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -26,7 +26,7 @@ typedef struct {
        khash_t(64) *hash;
        uint32_t format;
        int tid, len, last_pos;
-       int mask, min_mapQ;
+       int mask;
        char *ref;
        glfFile fp_glf; // for glf output only
 } pu_data_t;
@@ -280,7 +280,7 @@ int bam_pileup(int argc, char *argv[])
        d->tid = -1; d->mask = BAM_DEF_MASK;
        d->c = bam_maqcns_init();
        d->ido = bam_maqindel_opt_init();
-       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:q:")) >= 0) {
+       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:")) >= 0) {
                switch (c) {
                case 's': d->format |= BAM_PLF_SIMPLE; break;
                case 't': fn_list = strdup(optarg); break;
@@ -297,7 +297,6 @@ int bam_pileup(int argc, char *argv[])
                case 'g': d->format |= BAM_PLF_GLF; break;
                case 'I': d->ido->q_indel = atoi(optarg); break;
                case 'G': d->ido->r_indel = atof(optarg); break;
-               case 'q': d->min_mapQ = atoi(optarg); break;
                default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1;
                }
        }
@@ -307,7 +306,6 @@ int bam_pileup(int argc, char *argv[])
                fprintf(stderr, "Option: -s        simple (yet incomplete) pileup format\n");
                fprintf(stderr, "        -i        only show lines/consensus with indels\n");
                fprintf(stderr, "        -m INT    filtering reads with bits in INT [%d]\n", d->mask);
-               fprintf(stderr, "        -q INT    filtering reads with mapping quality smaller than INT [%d]\n", d->min_mapQ);
                fprintf(stderr, "        -M INT    cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
                fprintf(stderr, "        -t FILE   list of reference sequences (assume the input is in SAM)\n");
                fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
@@ -344,7 +342,7 @@ int bam_pileup(int argc, char *argv[])
                }
                d->h = fp->header;
                if (fn_pos) d->hash = load_pos(fn_pos, d->h);
-               sampileup(fp, d->mask, d->min_mapQ, pileup_func, d);
+               sampileup(fp, d->mask, pileup_func, d);
                samclose(fp); // d->h will be destroyed here
        }