#define MPLP_NO_COMP 0x20
#define MPLP_NO_ORPHAN 0x40
#define MPLP_REALN 0x80
+#define MPLP_SAMINFO 0x100
typedef struct {
int max_mq, min_mq, flag, min_baseQ, capQ_thres;
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
bcf_call_combine(gplp.n, bcr, ref16, &bc);
- bcf_call2bcf(tid, pos, &bc, b);
+ bcf_call2bcf(tid, pos, &bc, b, (conf->flag&MPLP_SAMINFO)? bcr : 0);
bcf_write(bp, bh, b);
bcf_destroy(b);
} else {
mplp.min_baseQ = 13;
mplp.capQ_thres = 0;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
- while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:B")) >= 0) {
+ while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BI")) >= 0) {
switch (c) {
case 'f':
mplp.fai = fai_load(optarg);
case 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break;
case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
case 'R': mplp.flag |= MPLP_REALN; break;
+ case 'I': mplp.flag |= MPLP_SAMINFO; 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, " -g generate BCF output\n");
fprintf(stderr, " -u do not compress BCF output\n");
fprintf(stderr, " -B disable BAQ computation\n");
+ fprintf(stderr, " -I additional individual information (DP and ST)\n");
fprintf(stderr, "\n");
fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
return 1;