typedef struct {
int max_mq, min_mq, flag, min_baseQ, capQ_thres;
- double theta;
char *reg, *fn_pos;
faidx_t *fai;
kh_64_t *hash;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
mplp.max_mq = 60;
- mplp.theta = 1e-3;
mplp.min_baseQ = 13;
mplp.capQ_thres = 0;
- while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:uaORC:")) >= 0) {
+ while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:")) >= 0) {
switch (c) {
- case 't': mplp.theta = atof(optarg); break;
case 'f':
mplp.fai = fai_load(optarg);
if (mplp.fai == 0) return 1;
case 'r': mplp.reg = strdup(optarg); break;
case 'l': mplp.fn_pos = strdup(optarg); break;
case 'g': mplp.flag |= MPLP_GLF; break;
- case 'u': mplp.flag |= MPLP_NO_COMP; break;
+ case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
case 'R': mplp.flag |= MPLP_REALN; 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, " -t FLOAT scaled mutation rate [%lg]\n", mplp.theta);
fprintf(stderr, " -g generate BCF output\n");
fprintf(stderr, " -u do not compress BCF output\n");
fprintf(stderr, "\n");