Added the -d option to limit maximum depth for indels.

diff --git a/bam_plcmd.c b/bam_plcmd.c
index ccc5eb95a8c397b76729f0d2ff3ce3ea4da77fdc..f8ae6b451f2f1d1da9a2b17d6c7085f4f5f2600c 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -31,6 +31,7 @@ typedef struct {
        uint32_t format;
        int tid, len, last_pos;
        int mask;
+    int max_depth;  // for indel calling, ignore reads with the depth too high. 0 for unlimited
        char *ref;
        glfFile fp_glf; // for glf output only
 } pu_data_t;
@@ -124,10 +125,11 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
        g3->offset = pos - d->last_pos;
        d->last_pos = pos;
        glf3_write1(d->fp_glf, g3);
-       if (pos < d->len) {
+    if (pos < d->len) {
+        int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth;
                if (proposed_indels)
-                       r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
-               else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
+                       r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
+               else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0);
        }
        if (r) { // then write indel line
                int het = 3 * n, min;
@@ -205,10 +207,11 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                        cns = b<<28 | 0xf<<24 | rmsQ<<16 | 60<<8;
                } else cns = bam_maqcns_call(n, pu, d->c);
        }
-       if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels
-               if (proposed_indels) // the first element gives the size of the array
-                       r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
-               else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
+    if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels
+        int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth;
+        if (proposed_indels) // the first element gives the size of the array
+            r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
+        else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0);
        }
        // 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)) {
@@ -319,10 +322,11 @@ int bam_pileup(int argc, char *argv[])
        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->max_depth = 0;
        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:S2aR:")) >= 0) {
+       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:")) >= 0) {
                switch (c) {
                case 'a': d->c->is_soap = 1; break;
                case 's': d->format |= BAM_PLF_SIMPLE; break;
@@ -333,6 +337,7 @@ int bam_pileup(int argc, char *argv[])
                case 'N': d->c->n_hap = atoi(optarg); break;
                case 'r': d->c->het_rate = atof(optarg); break;
                case 'M': d->c->cap_mapQ = atoi(optarg); break;
+               case 'd': d->max_depth = atoi(optarg); break;
                case 'c': d->format |= BAM_PLF_CNS; break;
                case 'i': d->format |= BAM_PLF_INDEL_ONLY; break;
                case 'v': d->format |= BAM_PLF_VAR_ONLY; break;
@@ -362,6 +367,7 @@ int bam_pileup(int argc, char *argv[])
                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, "        -M INT    cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
+        fprintf(stderr, "        -d INT    limit maximum depth for indels [unlimited]\n");
                fprintf(stderr, "        -t FILE   list of reference sequences (force -S)\n");
                fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
                fprintf(stderr, "        -f FILE   reference sequence in the FASTA format\n\n");