-h, --help                        Display this message and quit

  --version                         Display the version and quit

  gtf                               The input GTF file containing features
                                    to check the bam against

  bam                               The input SAM/BAM file containing reads
                                    to process

  output                            Output directory

  -s[sample], --sample=[sample]     The name of the current sample. Default:
                                    The bam's filename

  --bed=[BEDFILE]                   Optional input BED file containing
                                    non-overlapping exons used for fragment
                                    size calculations

  --chimeric-distance=[DISTANCE]    Set the maximum accepted distance
                                    between read mates. Mates beyond this
                                    distance will be counted as chimeric
                                    pairs. Default: 2000000 [bp]

  --fragment-samples=[SAMPLES]      Set the number of samples to take when
                                    computing fragment sizes. Requires the
                                    --bed argument. Default: 1000000

  -q[QUALITY],
  --mapping-quality=[QUALITY]       Set the lower bound on read quality for
                                    exon coverage counting. Reads below this
                                    number are excluded from coverage
                                    metrics. Default: 255

  --base-mismatch=[MISMATCHES]      Set the maximum number of allowed
                                    mismatches between a read and the
                                    reference sequence. Reads with more than
                                    this number of mismatches are excluded
                                    from coverage metrics. Default: 6

  --offset=[OFFSET]                 Set the offset into the gene for the 3'
                                    and 5' windows in bias calculation. A
                                    positive value shifts the 3' and 5'
                                    windows towards eachother, while a
                                    negative value shifts them apart.
                                    Default: 150 [bp]

  --window-size=[SIZE]              Set the size of the 3' and 5' windows in
                                    bias calculation. Default: 100 [bp]

  --gene-length=[LENGTH]            Set the minimum size of a gene for bias
                                    calculation. Genes below this size are
                                    ignored in the calculation. Default:
                                    600 [bp]

  --legacy                          Use legacy read counting rules. Read
                                    counts match output of RNA-SeQC 1.1.9

  --stranded=[stranded]             Use strand-specific metrics. Only
                                    features on the same strand of a read
                                    will be considered. Allowed values are
                                    'RF', 'rf', 'FR', and 'fr'

  -v, --verbose                     Give some feedback about what's going
                                    on. Supply this argument twice for
                                    progress updates while parsing the bam

  -t[TAG...], --tag=[TAG...]        Filter out reads with the specified tag.

  --chimeric-tag=[TAG]              Reads marked with the specified tag will
                                    be labeled as Chimeric. Defaults to 'mC'
                                    for compatibility with STAR

  --exclude-chimeric                Exclude chimeric reads from the read
                                    counts

  -u, --unpaired                    Allow unpaired reads to be quantified.
                                    Required for single-end libraries

  --rpkm                            Output gene RPKM values instead of TPMs

  --coverage                        If this flag is provided, coverage
                                    statistics for each transcript will be
                                    written to a table. Otherwise, only
                                    summary coverage statistics are
                                    generated and added to the metrics table

  --coverage-mask=[SIZE]            Sets how many bases at both ends of a
                                    transcript are masked out when computing
                                    per-base exon coverage. Default: 500bp

  -d[threshold],
  --detection-threshold=[threshold] Number of counts on a gene to consider
                                    the gene 'detected'. Additionally, genes
                                    below this limit are excluded from 3'
                                    bias computation. Default: 5 reads

  "--" can be used to terminate flag options and force all following
  arguments to be treated as positional options