#define MPLP_NO_COMP 0x20
#define MPLP_NO_ORPHAN 0x40
#define MPLP_REALN 0x80
-#define MPLP_CAPQ 0x100
typedef struct {
- int max_mq, min_mq, flag, min_baseQ;
+ int max_mq, min_mq, flag, min_baseQ, capQ_thres;
double theta;
char *reg, *fn_pos;
faidx_t *fai;
typedef struct {
bamFile fp;
bam_iter_t iter;
- int min_mq, flag, ref_id;
+ int min_mq, flag, ref_id, capQ_thres;
char *ref;
} mplp_aux_t;
static int mplp_func(void *data, bam1_t *b)
{
extern int bam_realn(bam1_t *b, const char *ref);
- extern int bam_cap_mapQ(bam1_t *b, char *ref);
+ extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
mplp_aux_t *ma = (mplp_aux_t*)data;
int ret, skip = 0;
do {
if (ret < 0) break;
skip = 0;
if (has_ref && (ma->flag&MPLP_REALN)) bam_realn(b, ma->ref);
- if ((ma->flag&MPLP_CAPQ) && has_ref) {
- int q = bam_cap_mapQ(b, ma->ref);
+ if (has_ref && ma->capQ_thres > 10) {
+ int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres);
if (q < 0) skip = 1;
else if (b->core.qual > q) b->core.qual = q;
} else if (b->core.flag&BAM_FUNMAP) skip = 1;
data[i] = calloc(1, sizeof(mplp_aux_t));
data[i]->min_mq = conf->min_mq;
data[i]->flag = conf->flag;
+ data[i]->capQ_thres = conf->capQ_thres;
data[i]->fp = bam_open(fn[i], "r");
h_tmp = bam_header_read(data[i]->fp);
bam_smpl_add(sm, fn[i], h_tmp->text);
mplp.max_mq = 60;
mplp.theta = 1e-3;
mplp.min_baseQ = 13;
- while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:uaORC")) >= 0) {
+ mplp.capQ_thres = 0;
+ while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:uaORC:")) >= 0) {
switch (c) {
case 't': mplp.theta = atof(optarg); break;
case 'f':
case 'u': mplp.flag |= MPLP_NO_COMP; break;
case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
- case 'C': mplp.flag |= MPLP_CAPQ; break;
case 'R': mplp.flag |= MPLP_REALN; break;
+ case 'C': mplp.capQ_thres = atoi(optarg); break;
case 'M': mplp.max_mq = atoi(optarg); break;
case 'q': mplp.min_mq = atoi(optarg); break;
case 'Q': mplp.min_baseQ = atoi(optarg); break;