+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
+ fprintf(stderr, "Options: -f FILE reference sequence file [null]\n");
+ fprintf(stderr, " -r STR region in which pileup is generated [null]\n");
+ fprintf(stderr, " -l FILE list of positions (format: chr pos) [null]\n");
+ fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
+ 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, " -c generate VCF output (consensus calling)\n");
+ fprintf(stderr, " -v show variant sites only\n");
+ fprintf(stderr, " -S calculate AFS (slow, to stderr)\n");
+ fprintf(stderr, " -2 conditional prior\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n");