#define MPLP_FMT_SP 0x200
typedef struct {
- int max_mq, min_mq, flag, min_baseQ, capQ_thres;
+ int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
char *reg, *fn_pos;
faidx_t *fai;
kh_64_t *hash;
static int mpileup(mplp_conf_t *conf, int n, char **fn)
{
mplp_aux_t **data;
- int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid;
+ int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth;
const bam_pileup1_t **plp;
bam_mplp_t iter;
bam_header_t *h = 0;
}
ref_tid = -1; ref = 0;
iter = bam_mplp_init(n, mplp_func, (void**)data);
+ max_depth = conf->max_depth;
+ if (max_depth * sm->n > 1<<20)
+ fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__);
+ if (max_depth * sm->n < 8000) {
+ max_depth = 8000 / sm->n;
+ fprintf(stderr, "<%s> Set max per-sample depth to %d\n", __func__, max_depth);
+ }
+ bam_mplp_set_maxcnt(iter, max_depth);
while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
if (hash) {
mplp.max_mq = 60;
mplp.min_baseQ = 13;
mplp.capQ_thres = 0;
+ mplp.max_depth = 250;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
- while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDS")) >= 0) {
+ while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDSd:")) >= 0) {
switch (c) {
case 'f':
mplp.fai = fai_load(optarg);
if (mplp.fai == 0) return 1;
break;
+ case 'd': mplp.max_depth = atoi(optarg); break;
case 'r': mplp.reg = strdup(optarg); break;
case 'l': mplp.fn_pos = strdup(optarg); break;
case 'g': mplp.flag |= MPLP_GLF; break;
fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
fprintf(stderr, " -Q INT min base quality [%d]\n", mplp.min_baseQ);
fprintf(stderr, " -q INT filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
+ fprintf(stderr, " -d INT max per-sample depth [%d]\n", mplp.max_depth);
fprintf(stderr, " -g generate BCF output\n");
fprintf(stderr, " -u do not compress BCF output\n");
fprintf(stderr, " -B disable BAQ computation\n");