* samtools-0.1.4-21 (r368)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 96f5c459df9dd88aa35d69a361898739016875d8..d18716ff72164ea9d8c9ad63efad9e1b308a28f2 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;
@@ -189,8 +189,10 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
        // when only variant sites are asked for, test if the site is a variant
        if ((d->format & BAM_PLF_CNS) && (d->format & BAM_PLF_VAR_ONLY)) {
                if (!(bam_nt16_table[rb] != 15 && cns>>28 != bam_nt16_table[rb])) { // not a SNP
-                       if (!(r && (r->gt == 2 || strcmp(r->s[r->gt], "*")))) // not an indel
+                       if (!(r && (r->gt == 2 || strcmp(r->s[r->gt], "*")))) { // not an indel
+                               if (r) bam_maqindel_ret_destroy(r);
                                return 0;
+                       }
                }
        }
        // print the first 3 columns
@@ -274,13 +276,13 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 
 int bam_pileup(int argc, char *argv[])
 {
-       int c;
+       int c, is_SAM = 0;
        char *fn_list = 0, *fn_fa = 0, *fn_pos = 0;
        pu_data_t *d = (pu_data_t*)calloc(1, sizeof(pu_data_t));
        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:S")) >= 0) {
                switch (c) {
                case 's': d->format |= BAM_PLF_SIMPLE; break;
                case 't': fn_list = strdup(optarg); break;
@@ -297,17 +299,18 @@ 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;
+               case 'S': is_SAM = 1; break;
                default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1;
                }
        }
+       if (fn_list) is_SAM = 1;
        if (optind == argc) {
                fprintf(stderr, "\n");
                fprintf(stderr, "Usage:  samtools pileup [options] <in.bam>|<in.sam>\n\n");
                fprintf(stderr, "Option: -s        simple (yet incomplete) pileup format\n");
+               fprintf(stderr, "        -S        the input is in SAM\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");
@@ -337,14 +340,14 @@ int bam_pileup(int argc, char *argv[])
                fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");
        {
                samfile_t *fp;
-               fp = fn_list? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);
+               fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);
                if (fp == 0 || fp->header == 0) {
                        fprintf(stderr, "[bam_pileup] fail to read the header: non-exisiting file or wrong format.\n");
                        return 1;
                }
                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
        }