h->target_len[i] = h0->target_len[i];
h->target_name[i] = strdup(h0->target_name[i]);
}
+ if (h0->rg2lib) h->rg2lib = bam_strmap_dup(h0->rg2lib);
return h;
}
fp->header = sam_header_read2((const char*)aux);
}
if (fp->header->n_targets == 0)
- fprintf(stderr, "[samopen] empty header.\n");
+ fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
} else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
}
+ sam_header_parse_rg(fp->header);
} else if (mode[0] == 'w') { // write
fp->header = bam_header_dup((const bam_header_t*)aux);
if (mode[1] == 'b') { // binary
+ char bmode[3];
+ bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
fp->type |= TYPE_BAM;
- fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w");
+ fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
if (fp->x.bam == 0) goto open_err_ret;
bam_header_write(fp->x.bam, fp->header);
} else { // text