fprintf(stderr, " -X output FLAG in string (samtools-C specific)\n");
fprintf(stderr, " -c print only the count of matching records\n");
fprintf(stderr, " -B collapse the backward CIGAR operation\n");
+ fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");
fprintf(stderr, " -L FILE output alignments overlapping the input BED FILE [null]\n");
fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n");
fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n");