int rflag_require, rflag_filter;
int openQ, extQ, tandemQ, min_support; // for indels
double min_frac; // for indels
- char *reg, *pl_list, *fai_fname;
+ char *reg, *pl_list, *fai_fname, *bcf_fname;
faidx_t *fai;
void *bed, *rghash;
} mplp_conf_t;
kstring_t s;
bh = calloc(1, sizeof(bcf_hdr_t));
s.l = s.m = 0; s.s = 0;
- bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w");
+ bp = bcf_open(conf->bcf_fname, (conf->flag&MPLP_NO_COMP)? "wu" : "w");
for (i = 0; i < h->n_targets; ++i) {
kputs(h->target_name[i], &s);
kputc('\0', &s);
mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
mplp.min_frac = 0.002; mplp.min_support = 1;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
+ mplp.bcf_fname="-";
static struct option lopts[] =
{
{"rf",1,0,1}, // require flag
{"ff",1,0,2}, // filter flag
+ {"output",1,0,(int)'c'}, // output flag
{0,0,0,0}
};
- while ((c = getopt_long(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV1:2:",lopts,NULL)) >= 0) {
+ while ((c = getopt_long(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV1:2:c:",lopts,NULL)) >= 0) {
switch (c) {
case 1 : mplp.rflag_require = strtol(optarg,0,0); break;
case 2 : mplp.rflag_filter = strtol(optarg,0,0); break;
case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
case 'O': mplp.flag |= MPLP_PRINT_POS; break;
+ case 'c': mplp.bcf_fname = strdup(optarg); 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;
fprintf(stderr, " -s output mapping quality (disabled by -g/-u)\n");
fprintf(stderr, " -S output per-sample strand bias P-value in BCF (require -g/-u)\n");
fprintf(stderr, " -u generate uncompress BCF output\n");
+ fprintf(stderr, " -c, --output=FILE output filename [stdout]\n");
fprintf(stderr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n");
fprintf(stderr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
fprintf(stderr, " -F FLOAT minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);